https://www.slicer.org/w/api.php?action=feedcontributions&user=Nicole&feedformat=atomSlicer Wiki - User contributions [en]2024-03-28T12:10:03ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/Nightly/Announcements&diff=47260Documentation/Nightly/Announcements2016-10-11T20:31:02Z<p>Nicole: /* Slicer Extensions */</p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
__NOTOC__<br />
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{|width="100%"<br />
|align="center"|<br />
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]<br />
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{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"<br />
|[[#Summary|Summary ]]<br />
|[[#What is 3D Slicer|What is 3D Slicer]]<br />
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]<br />
|[[#Slicer Training|Slicer Training]]<br />
|[[#Slicer Extensions|Slicer Extensions]]<br />
|[[#Other Improvements, Additions & Documentation|Other Improvements, Additions & Documentation]]<br />
|}<br />
<br />
= Summary = <br />
<br />
The community of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.<br />
<br />
<br><hr><br><br />
<br />
The development of Slicer, including its numerous modules, extensions, datasets, patches sent on user and developer lists, issues reports, suggestions, ... is made possible by awesome users, developers, contributors, commercial partners from around the world and also invaluable grants and funding agencies.<br />
<br />
For more details, see [[Documentation/{{documentation/version}}/Acknowledgments|Acknowledgments]] page.<br />
<br />
<br><hr><br><br />
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* Slicer {{documentation/version}} introduces <br />
<!--<br />
** An improved App Store, known as the Extension Manager, for adding plug-ins to Slicer. More than 80 plug-ins and packages of plug-ins are currently available.<br />
--><br />
** Close to XXX feature improvements and bug fixes have resulted in improved performance and stability.<br />
** Improvements to many modules.<br />
<br />
* Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and the bug tracker. <br />
* Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.<br />
* The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of tutorials and data sets for training in the use of Slicer. <br />
<br />
* [http://www.slicer.org slicer.org] is the portal to the application, training materials, and the development community.<br />
<br />
= What is 3D Slicer =<br />
{{:Documentation/{{documentation/version}}/Slicer}}<br />
<br />
= Citing Slicer =<br />
{{:Documentation/{{documentation/version}}/Acknowledgments/CitingSlicer}}<br />
<br />
= Slicer {{documentation/version}} Highlights =<br />
<br />
<gallery caption="New and Improved Modules" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:SlicerDMRIScreenshot.jpg| Introduced [[Documentation/Nightly/Extensions/SlicerDMRI|SlicerDMRI]] extension including diffusion MRI modules formerly in Slicer core and new functionality:<ul><li>DICOM tractography import/export</li><li>Improved diffusion brain mask generation</li><li>UKF multi-fiber tractography now available on Windows</li><li>Improved user interface and documentation</li></ul><br />
<br />
Image:SlicerProstate_Logo_1.0_128x128.png| Improved [[Documentation/Nightly/Extensions/SlicerProstate|SlicerProstate]] extension.<ul><li>improved reporting of DWI model fit diagnostics</li><li>refactoring of the code to separate functionality common to mpReview and SliceTracker extensions into a reusable library</li></ul><br />
<br />
Image:MpReview-Prostate.gif|New [[Documentation/Nightly/Extensions/mpReview|mpReview]] extension to support review and annotation of multiparametric image data. The driving use case for the development of this module was review and segmentation of the regions of interest in prostate cancer multiparametric MRI.<br />
<br />
Image:Needle_tracking.png| New [[Documentation/Nightly/Extensions/SliceTracker|SliceTracker]] extension to support navigation and guidance during in-bore MRI-guided prostate biopsy. Main documentation for this module is hosted on Gitbook - give us your feedback about this approach for documenting Slicer functionality! https://fedorov.gitbooks.io/slicetracker/content/<br />
<br />
Image:SlicerPathologyScreenShot9.png|New [[Documentation/Nightly/Extensions/SlicerPathology|SlicerPathology]] extension for tools for automatic and semi-automatic pathology image segmentation, with the interface to [http://imaging.cci.emory.edu/wiki/display/CAMIC/Home caMicroscope].<br />
<br />
</gallery><br />
<br />
= Slicer Training =<br />
<br />
The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of updated tutorials and data sets for training in the use of Slicer {{documentation/version}}. <br />
<br />
The first 3D Slicer training events using Slicer 4.5 will be organized at [http://www.na-mic.org/Wiki/index.php/MGH_2015 Massachusetts General Hospital (MGH), Boston, MA], [http://www.na-mic.org/Wiki/index.php/Brown_2015 Brown University, Providence, RI] and [http://www.na-mic.org/Wiki/index.php/RSNA_2015 RSNA 2015, Chicago, Il].<br />
<br />
<gallery caption="New Tutorials" widths="250px" heights="150px"><br />
<br />
Image:SlicerYouTube.png| [https://www.youtube.com/channel/UC11x1iQ7ydSIFYw4L6wveXg?view_as=public 3D Slicer YouTube channel] has been reorganized, new videos developed by the 3D Slicer community added to the channel {{new}}<br />
<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
<br />
</gallery><br />
<br />
=Slicer Extensions=<br />
<br />
<gallery caption="New Extensions" widths="250px" heights="150px"><br />
<br />
Image:AnglePlanes Logo.png|[[Documentation/{{documentation/version}}/Extensions/AnglePlanes|AnglePlanes]] This Module is used to calculate the angle between two planes by using the normals {{new}}<br />
<br />
Image:SlicerOpenCV-logo.png|[[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]] This Module provides a way for a Slicer extension developer use the OpenCV pacakge. {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
</gallery><br />
<br />
== Improved Extensions in Slicer 4.5 ==<br />
<br />
* [[Documentation/{{documentation/version}}/Extensions/CMFreg|CMFreg]]<br />
<!-- Add entry here --><br />
<br />
== Extensions removed from Slicer 4.5 ==<br />
<br />
<!-- * houghTransformCLI: Removed by the original author because it was not needed anymore. --><br />
<br />
== Extensions renamed ==<br />
<br />
<!-- <br />
* PyDevRemoteDebug -> [[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]]<br />
* MultidimData -> [[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]]<br />
* TrackerStabilizer -> [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Slicer-TrackerStabilizer]]<br />
* AirwaySegmentation -> [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Slicer-AirwaySegmentation]]<br />
--><br />
<br />
= Other Improvements, Additions & Documentation =<br />
<br />
== Optimization ==<br />
<br />
== Transforms ==<br />
<br />
== DICOM ==<br />
<br />
== Data processing ==<br />
<br />
== CLI ==<br />
<br />
== Usability ==<br />
<br />
== SubjectHierarchy ==<br />
<br />
== Python scripting ==<br />
<br />
== Editor ==<br />
<br />
== Markups ==<br />
<br />
== LabelMapVolumeNode ==<br />
<br />
== Slice viewers ==<br />
<br />
== DataProbe ==<br />
<br />
== SliceViewAnnotations ==<br />
<br />
== OpenIGTLink ==<br />
<br />
<br />
= For Developers =<br />
<br />
== Modules and Extensions ==<br />
<br />
<!-- <br />
* ExtensionWizard<br />
<br />
* SelfTests<br />
** Allow self tests to set a custom delay for message display<br />
<br />
* MRMLNodeComboBox<br />
** Allow qMRMLNodeComboBox base name setting for each node type <br />
** Added removeAttribute function to MRML node comboboxes and proxy model <br />
** Multiple node types can be created in qMRMLNodeComboBox <br />
** Support custom behavior for default actions. <br />
<br />
* MRML Scene introspection<br />
** Added node printself output to node inspector <br />
<br />
* Message logging<br />
** Added vtkInfoMacro<br />
<br />
* DICOM<br />
** Package additional DCMTK applications: echoscu, dsr2html, xml2dcm and xml2dsr<br />
<br />
* Markups<br />
** Signal end fiducial interaction in 3D <br />
** Add reusable simple markups widget <br />
<br />
* Module API<br />
** Extend module API with "widgetRepresentationCreationEnabled" property<br />
<br />
* Slicerlets<br />
** Allow slicelets and Slicer tests to handle log messages. <br />
<br />
* Units<br />
** Added extra units support: frequency, velocity and intensity.<br />
** Extended Units logic API adding GetDisplayCoefficient() and GetSIPrefixCoefficient() <br />
** Updated MRMLUnitNode to ensure value to string conversion account for precision. <br />
<br />
* SubjectHierarchy<br />
** Introduced adaptor classes facilitating implementation of python scripted subject hierarchy plugins. <br />
** Introduced autoDeleteSubjectHierarchyChildren property <br />
<br />
* Editor<br />
** Facilitate re-use of Editor python components in extension (LabelStructureListWidget in 043f398)<br />
** Updated EditUtil API adding function SetUseLabelOutline() to explicitly set label outline state on all Slice nodes<br />
--><br />
<br />
== Slicer Core ==<br />
<br />
<!-- <br />
* IDE integration<br />
** Improve build targets organization in IDE that support folders.<br />
** VisualStudio: Do not build documentation when F7 is pressed.<br />
** Facilitate integration with python IDE allowing minimal 'slicer' module to be imported.<br />
<br />
* Build-system<br />
** Add support for Visual Studio 2013.<br />
** Update build system anticipating transition to modern CMake.<br />
** Update MacOSX packaging infrastructure anticipating the signing of package in future release.<br />
** Update code base anticipitating compliance with C++11.<br />
** Remove <code>Slicer_ITKV3_COMPATIBILITY</code> build option.<br />
** Add option <code>Slicer_USE_ITKPython</code> to turn on ITK Python wrapping.<br />
** Removed duplicated code using ITK version of MGHIO.<br />
<br />
* Python<br />
** Added support writing scripted modules and widgets as new-style Python classes. <br />
** Simplify scripted module introducing SlicerPythonCppAPI. <br />
** Introduced qSlicerScriptedUtils::executeFile() <br />
** Updated CTK to include new PythonQt C++/Python ownership tracking feature. <br />
** Import scripted module as python module to avoid module top-level variables to clobber each other. [http://www.na-mic.org/Bug/view.php?id=3549 #3549]<br />
<br />
* Platform support<br />
** Fix support for 32-bit build allowing use of Slicer on Surface tablet.<br />
<br />
* Packaging & Testing infrastructure<br />
** Capturing VTK errors/warnings during testing.<br />
** Update extension build system to report packaging error on CDash.<br />
<br />
* Rendering / Visualization<br />
** Add Slicer_VTK_RENDERING_BACKEND configure option<br />
<br />
* MRML<br />
** Add support in vtkMRMLNode for multiple references to the same node. <br />
** Introducing InvokeCustomModifiedEvent. <br />
<br />
* ApplicationLogic<br />
** Added function PropagateLabelVolumeSelection(), PropagateForegroundVolumeSelection() and PropagateBackgroundVolumeSelection()<br />
<br />
* VolumeRenderingLogic<br />
** Extend volume rendering logic API adding GetPresetByName function. <br />
<br />
* View management<br />
** Add qMRMLLayoutViewFactory <br />
** Add utility method to display node in only 1 view <br />
<br />
* DICOM<br />
** [https://github.com/Slicer/Slicer/pull/359 upgraded DCMTK to the latest snapshot DCMTK-3.6.1_20150924]<br />
--><br />
<br />
<gallery caption="Improved Toolkits" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:CTK-Logo.png|Moved from CTK [https://github.com/commontk/CTK/commit/f64b68a f64b68a] to [https://github.com/commontk/CTK/commit/1c97e54 1c97e54] (499 commits) <!-- git log --oneline f64b68acd717dab060db41e8bee3f0f30df1a58f...1c97e5426f898bc7d074e6122992d0dd12bab56b --no-merges | wc -l --><br />
<br />
Image:CTKApplauncher_Logo.png|Moved from CTKAppLauncher v0.1.11 to v0.1.14 (43 commits) <!-- git log --oneline v0.1.11..v0.1.14 --no-merges | wc -l --><br />
<br />
Image:ITK_logo.png|Moved from ITK v4.4.1 to v4.6.0 (1089 commits) <!-- git log --oneline v4.4.1..56fae27 --no-merges | wc -l --><br />
<br />
Image:OpenIGTLink-Logo.png|Moved from OpenIGTLink [https://github.com/openigtlink/OpenIGTLink/compare/66e272d...849b434 66e272d to 849b434] (53 commits) <!-- git log --no-merges --oneline 66e272d..849b434 | wc -l --><br />
<br />
Image:Qt-logo.png |Moved from Qt 4.7.4 to Qt 4.8.6<br />
<br />
Image:VTK_logo.png|Moved from VTK v5.10.1 to VTK v6.2.0 (5490 commits) <!-- git log --oneline v5.10.1..b55dad7 --no-merges | wc -l --><br />
<br />
Image:DCMTK_logo.png|[https://github.com/Slicer/Slicer/pull/359 Upgraded DCMTK to DCMTK-3.6.1_20150924 snapshot]<br />
<br />
</gallery><br />
<br />
== Looking at the Code Changes ==<br />
<br />
From a git checkout you can easily see the all the commits since the time of the 4.4.0 release:<br />
<br />
git log v4.4.0..HEAD<br />
<br />
To see a summary of your own commits, you could use something like:<br />
<br />
git log v4.4.0..HEAD --oneline --author=me<br />
<br />
see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.<br />
<br />
[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]<br />
<br />
= Related Projects =<br />
<gallery caption="" widths="250px" heights="150px" perrow="3"><br />
</gallery></div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20161004&diff=47143Developer Meetings/201610042016-10-04T12:58:56Z<p>Nicole: Created page with "<br> {{mbox | type = style | text = If you would like to list your topic here, create a wiki account and [{{fullurl:{{FULLPAGENAME}}|action=edit}} edit t..."</p>
<hr />
<div><br><br />
{{mbox<br />
| type = style<br />
| text = If you would like to list your topic here, [[Special:UserLogin|create a wiki account]] and [{{fullurl:{{FULLPAGENAME}}|action=edit}} edit this page].<br />
| image= [[File:smile.png|40px]]<br />
}}<br />
<br><br />
<br />
= To Discuss=<br />
* Extensions with third party python libraries, running tests in both build and package directories<br />
* 4.6 Release schedule<br />
<br />
= Updates =<br />
<br />
= Conclusion =</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings&diff=47142Developer Meetings2016-10-04T12:57:40Z<p>Nicole: /* 2016 */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!--<br />
<center>[[File:ScreenShot_GoogleHangout.PNG|300px]]</center><br />
--><br />
<br />
== Introduction ==<br />
The Slicer engineering team is distributed across several locations. Because of this, we use a variety of electronic means for communication. In addition to the twice a year [http://wiki.na-mic.org/Wiki/index.php/Project_Events project weeks], and additional topic oriented meeting, we have a weekly Google hangout. <br />
<br />
These meetings are open to anyone. If you are interested, please join the [https://plus.google.com/u/1/communities/105715968666294296532 3DSlicer BarCamp] community on Google Plus.<br />
<br />
<br><br />
{{mbox<br />
| type = style<br />
| text = <big>Open to everyone - Every Tuesday @ 10am EST on [https://plus.google.com/u/0/communities/105715968666294296532/events 3DSlicer BarCamp] community</big><br />
| image= [[File:smile.png|40px]]<br />
}}<br />
<br><br />
<br />
<br />
<small>[[Developer_Meetings/OrganizerInstruction|How to schedule a hangout ?]]</small><br />
<br><small>[[Documentation/Nightly/FAQ/BarCamp#Moderators:_How_to_approve.2Freject_requests_.3F|Moderators:How to approve/reject requests?]]</small><br />
<br />
== 2016 ==<br />
* [[Developer_Meetings/20161004|Oct 4th, 2016]]<br />
* [[Developer_Meetings/20160920|Sept 20th, 2016]]<br />
* [[Developer_Meetings/20160913|Sept 13th, 2016]]<br />
* [[Developer_Meetings/20160906|Sept 06th, 2016]]<br />
* [[Developer_Meetings/20160830|August 30th, 2016]]<br />
* [[Developer_Meetings/20160823|August 23th, 2016]]<br />
* [[Developer_Meetings/20160816|August 16th, 2016]]<br />
* [[Developer_Meetings/20160809|August 9th, 2016]]<br />
* [[Developer_Meetings/20160726|July 26th, 2016]]<br />
* [[Developer_Meetings/20160719|July 19th, 2016]]<br />
* [[Developer_Meetings/20160712|July 12th, 2016]]<br />
* [[Developer_Meetings/20160705|July 5th, 2016]]<br />
* [[Developer_Meetings/20160628|June 28th, 2016]]<br />
* June 21st, 2016 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2016_Summer_Project_Week Winter project week]</small><br />
* [[Developer_Meetings/20160614|June 14th, 2016]]<br />
* [[Developer_Meetings/20160607|June 7th, 2016]]<br />
* [[Developer_Meetings/20160531|May 31st, 2016]]<br />
* May 24th, 2016 - <small>Cancelled - [http://qiicr.org/web/outreach/MIWS-hackfest MIWS Hackfest at BWH]</small><br />
* [[Developer_Meetings/20160517|May 17th, 2016]]<br />
* [[Developer_Meetings/20160510|May 10th, 2016]]<br />
* [[Developer_Meetings/20160425|April 25th, 2016]]<br />
* [[Developer_Meetings/20160419|April 19th, 2016]]<br />
* April 12th, 2016 - <small>Cancelled</small><br />
* [[Developer_Meetings/20160405|April 5th, 2016]]<br />
* [[Developer_Meetings/20160322|March 22nd, 2016]]<br />
* [[Developer_Meetings/20160315|March 15th, 2016]]<br />
* [[Developer_Meetings/20160308|March 8th, 2016]]<br />
* [[Developer_Meetings/20160301|March 1st, 2016]]<br />
* [[Developer_Meetings/20160223|February 23th, 2016]]<br />
* [[Developer_Meetings/20160216|February 16th, 2016]]<br />
* [[Developer_Meetings/20160209|February 9th, 2016]]<br />
* [[Developer_Meetings/20160202|February 2nd, 2016]]<br />
* [[Developer_Meetings/20160126|January 26th, 2016]]<br />
* [[Developer_Meetings/20160119|January 19th, 2016]]<br />
* [[Developer_Meetings/20160112|January 12th, 2016]]<br />
* January 5th, 2016 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2016_Winter_Project_Week Winter project week]</small><br />
<br />
== 2015 ==<br />
<br />
* December 29th, 2015 - <small>Canceled - Happy holidays</small><br />
* December 22nd, 2015 - <small>Canceled - Happy holidays</small><br />
* [[Developer_Meetings/20151215|December 15th, 2015]]<br />
* [[Developer_Meetings/20151215|December 15th, 2015]]<br />
* [[Developer_Meetings/20151208|December 8th, 2015]]<br />
* [[Developer_Meetings/20151201|December 1st, 2015]]<br />
* [[Developer_Meetings/20151124|November 24th, 2015]] - <small>KickOff for [http://www.na-mic.org/Wiki/index.php/2016_Winter_Project_Week 2016 Project Week @ Cambridge]</small><br />
* [[Developer_Meetings/20151117|November 17th, 2015]]<br />
* [[Developer_Meetings/20151110|November 10th, 2015]]<br />
* [[Developer_Meetings/20151103|November 3rd, 2015]]<br />
* [[Developer_Meetings/20151027|October 27th, 2015]]<br />
* [[Developer_Meetings/20151020|October 20th, 2015]]<br />
* [[Developer_Meetings/20151013|October 13th, 2015]]<br />
* [[Developer_Meetings/20151006|October 6th, 2015]]<br />
* [[Developer_Meetings/20150929|September 29th, 2015]]<br />
* [[Developer_Meetings/20150922|September 22nd, 2015]]<br />
* [[Developer_Meetings/20150915|September 15th, 2015]]<br />
* [[Developer_Meetings/20150908|September 8th, 2015]]<br />
* [[Developer_Meetings/20150901|September 1st, 2015]]<br />
* [[Developer_Meetings/20150825|August 25th, 2015]]<br />
* [[Developer_Meetings/20150818|August 18th, 2015]]<br />
* [[Developer_Meetings/20150811|August 11th, 2015]]<br />
* [[Developer_Meetings/20150804|August 4th, 2015]]<br />
* [[Developer_Meetings/20150728|July 28th, 2015]]<br />
* [[Developer_Meetings/20150714|July 14th, 2015]]<br />
* [[Developer_Meetings/20150707|July 7th, 2015]]<br />
* June 23rd, 2015 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Summer project week]</small><br />
* [[Developer_Meetings/20150616|June 16th, 2015]]<br />
* [[Developer_Meetings/20150609|June 9th, 2015]]<br />
* [[Developer_Meetings/20150602|June 2nd, 2015]]<br />
* [[Developer_Meetings/20150526|May 26th, 2015]]<br />
* [[Developer_Meetings/20150519|May 19th, 2015]]<br />
* [[Developer_Meetings/20150512|May 12th, 2015]]<br />
* [[Developer_Meetings/20150505|May 5th, 2015]]<br />
* [[Developer_Meetings/20150428|April 28st, 2015]]<br />
* [[Developer_Meetings/20150421|April 21st, 2015]]<br />
* [[Developer_Meetings/20150414|April 14th, 2015]]<br />
* [[Developer_Meetings/20150407|April 7th, 2015]]<br />
* [[Developer_Meetings/20150331|March 31st, 2015]]<br />
* [[Developer_Meetings/20150324|March 24th, 2015]]<br />
* [[Developer_Meetings/20150317|March 17th, 2015]]<br />
* [[Developer_Meetings/20150310|March 10th, 2015]]<br />
* [[Developer_Meetings/20150303|March 3rd, 2015]]<br />
* [[Developer_Meetings/20150224|February 24th, 2015]]<br />
* [[Developer_Meetings/20150224|February 24th, 2015]]<br />
* [[Developer_Meetings/20150217|February 17th, 2015]]<br />
* [[Developer_Meetings/20150210|February 10th, 2015]]<br />
* [[Developer_Meetings/20150203|February 3rd, 2015]]<br />
* [[Developer_Meetings/20150127|January 27th, 2015]]<br />
* [[Developer_Meetings/20150120|January 20th, 2015]]<br />
* [[Developer_Meetings/20150113|January 13th, 2015]]<br />
* January 6th, 2015 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Winter project week]</small><br />
<br />
== 2014 ==<br />
* [[Developer_Meetings/20141230|December 30th, 2014]]<br />
* [[Developer_Meetings/20141223|December 23rd, 2014]]<br />
* [[Developer_Meetings/20141216|December 16th, 2014]]<br />
* [[Developer_Meetings/20141209|December 9th, 2014]]<br />
* [[Developer_Meetings/20141202|December 2nd, 2014]]<br />
* [[Developer_Meetings/20141125|November 25th, 2014]]<br />
* [[Developer_Meetings/20141118|November 18th, 2014]]<br />
* [[Developer_Meetings/20141111|November 11th, 2014]]<br />
* [[Developer_Meetings/20141103|November 3rd, 2014]]<br />
* [[Developer_Meetings/20141029|October 29th, 2014]]<br />
* [[Developer_Meetings/20141021|October 21st, 2014]]<br />
* [[Developer_Meetings/20141014|October 14th, 2014]]<br />
* [[Developer_Meetings/20141007|October 7th, 2014]]<br />
* [[Developer_Meetings/20140930|September 30th, 2014]]<br />
* [[Developer_Meetings/20140923|September 23rd, 2014]]<br />
* [[Developer_Meetings/20140916|September 16th, 2014]]<br />
* [[Developer_Meetings/20140909|September 9th, 2014]]<br />
* [[Developer_Meetings/20140901|September 1st, 2014]]<br />
* [[Developer_Meetings/20140826|August 26th, 2014]]<br />
* [[Developer_Meetings/20140819|August 19th, 2014]]<br />
* [[Developer_Meetings/20140812|August 12th, 2014]]<br />
* [[Developer_Meetings/20140805|August 5th, 2014]]<br />
* [[Developer_Meetings/20140729|July 29th, 2014]]<br />
* [[Developer_Meetings/20140722|July 22nd, 2014]]<br />
* [[Developer_Meetings/20140715-2|July 15th, 2014]] <small>Developer hangout</small><br />
* [[Developer_Meetings/20140715|July 15th, 2014]] <small>Extension Developers - From VTK5 to VTK6 - Q&A- Google Hangout</small><br />
* [[Developer_Meetings/20140701|July 1st, 2014]]<br />
* June 24th, 2014 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week 19th NA-MIC project week]</small><br />
* [[Developer_Meetings/20140617|June 17th, 2014]]<br />
* [[Developer_Meetings/20140610|June 10th, 2014]]<br />
* [[Developer_Meetings/20140603|June 3rd, 2014]]<br />
* [[Developer_Meetings/20140527|May 27th, 2014]]<br />
* [[Developer_Meetings/20140520|May 20th, 2014]]<br />
* [[Developer_Meetings/20140513|May 13th, 2014]]<br />
* May 6th, 2014 - <small>Cancelled - [http://www.commontk.org/index.php/CTK-Hackfest-May-2014 CTK Hackfest in St Louis]</small><br />
* [[Developer_Meetings/20140429|April 29th, 2014]]<br />
* [[Developer_Meetings/20140422|April 22th, 2014]]<br />
* [[Developer_Meetings/20140415|April 15th, 2014]]<br />
* [[Developer_Meetings/20140408|April 8th, 2014]]<br />
* [[Developer_Meetings/20140401|April 1st, 2014]]<br />
* [[Developer_Meetings/20140325|March 25th, 2014]]<br />
* [[Developer_Meetings/20140318|March 18th, 2014]]<br />
* [[Developer_Meetings/20140311|March 11th, 2014]]<br />
* [[Developer_Meetings/2014030607|March 6-7, 2014 (Face to Face in Boston)]]<br />
* [[Developer_Meetings/20140304|March 4th, 2014]]<br />
* [[Developer_Meetings/20140225|February 25th, 2014]]<br />
* [[Developer_Meetings/20140218|February 18th, 2014]]<br />
* [[Developer_Meetings/20140211|February 11th, 2014]]<br />
* [[Developer_Meetings/20140204|February 4th, 2014]]<br />
* [[Developer_Meetings/20140128|January 28th, 2014]]<br />
* [[Developer_Meetings/20140121|January 21st, 2014]]<br />
* [[Developer_Meetings/20140114|January 14th, 2014]]<br />
* January 7th, 2014 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/AHM_2014 AHM in Salt Lake City]</small><br />
<br />
== 2013 ==<br />
* December 31th, 2013 - <small>Cancelled - New year day</small><br />
* December 24th, 2013 - <small>Cancelled - Christmas day</small><br />
* [[Developer_Meetings/20131217|December 17, 2013]]<br />
* [[Developer_Meetings/20131210|December 10, 2013]]<br />
* [[Developer_Meetings/20131203|December 3rd, 2013]]<br />
* [[Developer_Meetings/20131126|November 26th, 2013]]<br />
* [[Developer_Meetings/20131119|November 19th, 2013]]<br />
* [[Developer_Meetings/20131112|November 12th, 2013]]<br />
* [[Developer_Meetings/20131105|November 5th, 2013]]<br />
* [[Developer_Meetings/20131029|October 29th, 2013]]<br />
* [[Developer_Meetings/20131022|October 22th, 2013]]<br />
* [[Developer_Meetings/20131015|October 15th, 2013]]<br />
* [[Developer_Meetings/20131008|October 8th, 2013]]<br />
* [[Developer_Meetings/20131001|October 1st, 2013]]<br />
* [[Developer_Meetings/20130924|September 24th, 2013]]<br />
* [[Developer_Meetings/20130917|September 17th, 2013]]<br />
* [[Developer_Meetings/20130910|September 10th, 2013]]<br />
* [[Developer_Meetings/20130903|September 3rd, 2013]]<br />
* [[Developer_Meetings/20130827|August 27th, 2013]]<br />
* [[Developer_Meetings/20130820|August 20th, 2013]]<br />
* [[Developer_Meetings/20130813|August 13th, 2013]]<br />
* [[Developer_Meetings/20130806|August 6th, 2013]]<br />
* [[Developer_Meetings/20130730|July 30th, 2013]]<br />
* [[Developer_Meetings/20130723|July 23rd, 2013]]<br />
* [[Developer_Meetings/20130716|July 16th, 2013]]<br />
* [[Developer_Meetings/20130709|July 9th, 2013]]<br />
* [[Developer_Meetings/20130702|July 2nd, 2013]]<br />
* June 18th, 23rd 2013 - cancelled due to NA-MIC Project week<br />
* [[Developer_Meetings/20130611|June 11th, 2013]]<br />
* [[Developer_Meetings/20130604|June 4th, 2013]]<br />
* [[Developer_Meetings/20130528|May 28th, 2013]]<br />
* May 21th, 2013 - <small>Cancelled - [http://www.commontk.org/index.php/CTK-Hackfest-May-2013 CTK Hackfest in Canada]</small><br />
* [[Developer_Meetings/20130514|May 14th, 2013]]<br />
* [[Developer_Meetings/20130507|May 7th, 2013]]<br />
* [[Developer_Meetings/20130430|April 30th, 2013]]<br />
* [[Developer_Meetings/20130423|April 23th, 2013]]<br />
* [[Developer_Meetings/20130416|April 16th, 2013]]<br />
* [[Developer_Meetings/20130409|April 9th, 2013]]<br />
* [[Developer_Meetings/20130402|April 2nd, 2013]]<br />
* [[Developer_Meetings/20130326|March 26th, 2013]]<br />
* [[Developer_Meetings/20130319|March 19th, 2013]]<br />
* [[Developer_Meetings/20130312|March 12th, 2013]]<br />
* [[Developer_Meetings/20130305|March 05th, 2013]]<br />
* [[Developer_Meetings/20130226|February 26th, 2013]]<br />
* [[Developer_Meetings/20130219|February 19th, 2013]]<br />
* [[Developer_Meetings/20130212|February 12th, 2013]]<br />
* [[Developer_Meetings/20130205|February 5th, 2013]]<br />
* [[Developer_Meetings/20130129|January 29th, 2013]]<br />
* [[Developer_Meetings/20130122|January 22nd, 2013]]<br />
* January 15th, 2013 - <small>Cancelled - AHM happened previous week</small><br />
* January 8th, 2013 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/AHM_2013 AHM in Salt Lake City]</small><br />
* January 1st, 2013 - <small>Cancelled - New year day</small><br />
<br />
== 2012 ==<br />
* December 25th, 2012 - <small>Cancelled - Christmas day</small><br />
* [[Developer_Meetings/20121218|December 18th, 2012]]<br />
* [[Developer_Meetings/20121211|December 11th, 2012]]<br />
* [[Developer_Meetings/20121204|December 4th, 2012]]<br />
* [[Developer_Meetings/20121127|November 27th, 2012]]<br />
* [[Developer_Meetings/20121120|November 20th, 2012]]<br />
* [[Developer_Meetings/20121113|November 13th, 2012]]<br />
* [[Developer_Meetings/20121106|November 6th, 2012]]<br />
* [[Developer_Meetings/20121030|October 30th, 2012]]<br />
* [[Developer_Meetings/20121023|October 23th, 2012]]<br />
* [[Developer_Meetings/20121016|October 16th, 2012]]<br />
* [[Developer_Meetings/20121009|October 09th, 2012]]<br />
* [[Developer_Meetings/20121002|October 02th, 2012]]<br />
* [[Developer_Meetings/20120925|September 25th, 2012]]<br />
* [[Developer_Meetings/20120918|September 18th, 2012]]<br />
* [[Developer_Meetings/20120911|September 11th, 2012]]<br />
* [[Developer_Meetings/20120904|September 4th, 2012]]<br />
* [[Developer_Meetings/20120828|August 28th, 2012]]<br />
* [[Developer_Meetings/20120821|August 21st, 2012]]<br />
* [[Developer_Meetings/20120814|August 14th, 2012]]<br />
* [[Developer_Meetings/20120807|August 7th, 2012]]<br />
* [[Developer_Meetings/20120731|July 31th, 2012]]<br />
* [[Developer_Meetings/20120724|July 24th, 2012]]<br />
* [[Developer_Meetings/20120717|July 17th, 2012]]<br />
* [[Developer_Meetings/20120710|July 10th, 2012]]<br />
* [[Developer_Meetings/20120703|July 3rd, 2012]]<br />
* [[Developer_Meetings/20120626|June 26th, 2012]]<br />
* [[Developer_Meetings/20120619|June 19th, 2012]]<br />
* [[Developer_Meetings/20120612|June 12th, 2012]]<br />
* [[Developer_Meetings/20120605|June 5th, 2012]]<br />
* [[Developer_Meetings/20120529|May 29, 2012]]<br />
* [[Developer_Meetings/20120522|May 22, 2012]]<br />
* [[Developer_Meetings/20120515|May 15, 2012]]<br />
* [[Developer_Meetings/20120508|May 8, 2012]]<br />
* [[Developer_Meetings/20120501|May 1st, 2012]]<br />
<br />
=== Miscellaneous ===<br />
* [http://wiki.na-mic.org/Wiki/index.php/Slicer4.2Planning August 20st, 2012 - Slicer 4.2 planning]<br />
<br />
== 2010 - 2011 ==<br />
* See [[Slicer4:QtPort/MeetingNotes]]<br />
<br />
== 2009 ==<br />
* September 16-17: [[Slicer:Developer_Meetings:20090916|Slicer widgets brainstorming]] (rough notes)<br />
* February 3: [[Slicer:Developer_Meetings:20090203|mBIRN preparation, Slicer3.4 release]]<br />
<br />
== 2008 ==<br />
* September 16: Demian on Python/Tractography<br />
* August 26: [[Slicer:Developer_Meetings:20080826|Slicer and NA-MIC Overview]]<br />
* August 11: [http://www.na-mic.org/Wiki/index.php/Slicer3_Q%26A_2008-11-18 Introduction of new researchers and developers (17 attendees)]<br />
* July 29: [[Slicer:Developer_Meetings:20080729|Slicer 3.2 release]]<br />
<br />
== 2007 ==<br />
* July 16: [[Slicer:Developer_Meetings:20070716|PNL demo Slicer3]]<br />
* June 12: [[Slicer:Developer_Meetings:20070612|PNL wishlist for Slicer3]]<br />
* March 27: [[Slicer:Developer_Meetings:20070327|Slicer 2.7, Slicer3 beta]]<br />
* February 6: [[Slicer:Developer_Meetings:20070206|Slicer3 mBIRN meeting Prep]]<br />
* January 30: [[Slicer:Developer_Meetings:20070130|Slicer3 Release Planning]]<br />
* January 2: [[Slicer:Developer_Meetings:20070102|Slicer3 AHM Prep]]<br />
<br />
== 2006 ==<br />
* November 21: [[Slicer:Developer_Meetings:20061121|Slicer3 Updates, preparations for retreat]]<br />
* November 07: [[Slicer:Developer_Meetings:20061107|Slicer3 Updates, NA-MIC Mesh Kickoff]]<br />
* October 10: [[Slicer:Developer_Meetings:20061010| Slicer3 Updates]]<br />
* August 29: [[Slicer:Developer_Meetings:20060829|Slicer 3 and Slicer 2.6 bugs]]<br />
* May 2: [[Slicer:Developer_Meetings:20060502|Release 2.6, Fiducials, Slicer for MRT]]<br />
* March 14: [[Slicer:Developer_Meetings:20060314|Release 2.6, mBIRN meeting, Slicer MRT]]<br />
<br />
<br />
== 2005 ==<br />
* June 7: [[Slicer:Developer_Meetings:20050607|NA-MIC Programming Week discussion: Slicer 3]]<br />
* May 24: [[Slicer:Developer_Meetings:20050524|Release 2.5]]<br />
* May 10: [[Slicer:Developer_Meetings:20050510|Release 2.5]]<br />
* April 11: [[Slicer:Developer_Meetings:20050411|To-do list for release 2.5, OpenTracker]]<br />
* March 29: [[Slicer:Developer_Meetings:20050329|Dan Kacher : Integrating trackers with Slicer ]]<br />
* March 15: [[Slicer:Developer_Meetings:20050315|Updates from BIRN Meeting, Training, Windows Building, Release 2.5]]<br />
* March 1: [[Slicer:Developer_Meetings:20050301|Updates from NA-MIC Meeting, Current and Future Projects]]<br />
* February 1: [[Slicer:Developer_Meetings:20050201|Randy Ellis : demo of surgical navigation system]]<br />
* January 18: [[Slicer:Developer_Meetings:20050118|Slicer Architecture]]</div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerOpenCV&diff=47129Documentation/Nightly/Extensions/SlicerOpenCV2016-09-29T21:43:25Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contributor1: Andrey Fedorov ({{collaborator|name|spl}})<br><br />
Contributor2: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:SlicerOpenCV-logo.png|x200px]]<br />
<br />
This extension provides a way for a Slicer extension developer to build against the OpenCV pacakge, by depending on the SlicerOpenCV extension. <br />
[http://opencv.org OpenCV] (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* If an extension developer needs the algorithms provided by OpenCV, they can add a module dependency on SlicerOpenCV and obtain a Slicer-style library to link against and use.<br />
** SlicerOpenCV also provides a python wrapped OpenCV library that can be used in scripted modules.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
* A Python scripted module is provided in the SlicerOpenCV extension to provide an example on how to use OpenCV from within scripted modules in Slicer:<br />
** [https://github.com/SBU-BMI/SlicerOpenCV/blob/master/SlicerOpenCV/Testing/Python/SlicerOpenCVSelfTest.py SlicerOpenCVSelfTest.py] (note: this self test will run from inside the Slicer GUI when Developer Mode has been enabled, but it currently won't run as a ctest command line test)<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The OpenCV module doesn't provide a GUI, it's intended to be used at the library level by other modules.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
* The [[Documentation/{{documentation/version}}/Extensions/OpenCVExample | OpenCVExample]] extension depends on this module and provides a template for linking and using OpenCV.<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]<br />
* [http://opencv.org Open Source Computer Vision] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
While configuring your project that depends on a built version of SlicerOpenCV, you need to set SlicerOpenCV_DIR to point to SlicerOpenCV_BUILD_DIR/inner-build - this is the location of SlicerOpenCVConfig.cmake<br />
<br />
Include the SlicerOpenCV extension by calling find_package(SlicerOpenCV REQUIRED). This will set OpenCV_DIR in the scope of your extension.<br />
<br />
This extension also provides the ITK module Video Bridge OpenCV [http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/VideoProcessingUsingOpenCVBridge/index.html Video Processing Using OpenCV Bridge]<br />
<br />
===C++===<br />
<br />
Once the library is available, in C++ you can include header files and use the video IO factory through ITK to read from file:<br />
<br />
itk::VideoIOBase::Pointer ioReadFile = itk::VideoIOFactory::CreateVideoIO(<br />
itk::VideoIOFactory::ReadFileMode, input);<br />
if (!ioReadFile)<br />
{<br />
std::cerr << "Did not create valid VideoIO for reading from file " << std::endl;<br />
return;<br />
}<br />
<br />
You can also use the OpenCV library directly to access an attached camera:<br />
<br />
itk::SizeValueType cameraNumber = 0;<br />
CvCapture* cameraCapture = cvCaptureFromCAM( cameraNumber );<br />
if (cameraCapture == ITK_NULLPTR)<br />
{<br />
std::cerr << "Unable to create a camera to capture from" << std::endl;<br />
return;<br />
}<br />
}<br />
<br />
===Python===<br />
<br />
SlicerOpenCV also provides the python wrapped OpenCV library. It's bundled in the extension in the lib/Slicer-X.Y directory. A Python scripted self test was added to the SlicerOpenCV module, [https://github.com/SBU-BMI/SlicerOpenCV/tree/master/SlicerOpenCV/Testing/Python Python tests], to provide an example of how to use the python module:<br />
<br />
import cv2<br />
<br />
Note: there's some work to be done on Slicer's Python infrastructure to ensure that this always works in installed extensions with third party libraries (PYTHONPATH needs to be set correctly). A work around as illustrated as a case in the SlicerOpenCVSelfTest script is to use an explicit path to the wrapped library, cv2File, adn load it directly:<br />
<br />
cv2 = imp.load_dynamic('cv2', cv2File)<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20160913&diff=47040Developer Meetings/201609132016-09-13T14:34:52Z<p>Nicole: </p>
<hr />
<div><br><br />
{{mbox<br />
| type = style<br />
| text = If you would like to list your topic here, [[Special:UserLogin|create a wiki account]] and [{{fullurl:{{FULLPAGENAME}}|action=edit}} edit this page].<br />
| image= [[File:smile.png|40px]]<br />
}}<br />
<br><br />
<br />
= To Discuss=<br />
* OpenGL backend 2D actor ordering issue http://www.na-mic.org/Bug/view.php?id=4251<br />
* Testing a python wrapped library in an extension (Nicole)<br />
** On windows, I can currently get the python test to run against a third party python wrapped shared library via the GUI as a self test, but not from the build directory as a self test (on mac, doing a load_dynamic with the full path works, but not on win64). <br />
** https://github.com/naucoin/SlicerOpenCV/commit/82fce00a5b94cfbf29288c8e21ee8bef3d8c67d0#diff-ddfa6f551f1d1daf3e597517872be13bR15<br />
** pull request: https://github.com/SBU-BMI/SlicerOpenCV/pull/39<br />
* Request for quarterly releases http://massmail.spl.harvard.edu/public-archives/slicer-devel/2016/040732.html<br />
** To discuss: what work is required for a release and how can it be streamlined?<br />
<br />
= Updates =<br />
# Greg to update on infrastructure and wiki migration<br />
<br />
= Conclusion =<br />
* Greg will make the repository storing the ansible role public. Next we will look into transferring to the Slicer organization.</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20160913&diff=46999Developer Meetings/201609132016-09-09T21:38:39Z<p>Nicole: /* To Discuss */</p>
<hr />
<div><br><br />
{{mbox<br />
| type = style<br />
| text = If you would like to list your topic here, [[Special:UserLogin|create a wiki account]] and [{{fullurl:{{FULLPAGENAME}}|action=edit}} edit this page].<br />
| image= [[File:smile.png|40px]]<br />
}}<br />
<br><br />
<br />
= To Discuss=<br />
* OpenGL backend 2D actor ordering issue http://www.na-mic.org/Bug/view.php?id=4251<br />
* Testing a python wrapped library in an extension (Nicole)<br />
** On windows, I can currently get the python test to run against a third party python wrapped shared library via the GUI as a self test, but not from the build directory as a self test (on mac, doing a load_dynamic with the full path works, but not on win64). <br />
** https://github.com/naucoin/SlicerOpenCV/commit/82fce00a5b94cfbf29288c8e21ee8bef3d8c67d0#diff-ddfa6f551f1d1daf3e597517872be13bR15<br />
<br />
= Updates =<br />
<br />
= Conclusion =</div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerOpenCV&diff=45605Documentation/Nightly/Extensions/SlicerOpenCV2016-05-26T18:30:45Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contributor1: Andrey Fedorov ({{collaborator|name|spl}})<br><br />
Contributor2: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:SlicerOpenCV-logo.png|x200px]]<br />
<br />
This extension provides a way for a Slicer extension developer to build against the OpenCV pacakge, by depending on the SlicerOpenCV extension. <br />
[http://opencv.org OpenCV] (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* If an extension developer needs the algorithms provided by OpenCV, they can add a module dependency on SlicerOpenCV and obtain a Slicer style library to link against and use.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The OpenCV module doesn't provide a GUI, it's intended to be used at the library level by other modules.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
* The [[Documentation/{{documentation/version}}/Extensions/OpenCVExample | OpenCVExample]] extension depends on this module and provides a template for linking and using OpenCV.<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]<br />
* [http://opencv.org Open Source Computer Vision] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
While configuring your project that depends on a built version of SlicerOpenCV, you need to set SlicerOpenCV_DIR to point to SlicerOpenCV_BUILD_DIR/inner-build - this is the location of SlicerOpenCVConfig.cmake<br />
<br />
Include the SlicerOpenCV extension by calling find_package(SlicerOpenCV REQUIRED). This will set OpenCV_DIR in the scope of your extension.<br />
<br />
This extension also provides the ITK module Video Bridge OpenCV [http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/VideoProcessingUsingOpenCVBridge/index.html Video Processing Using OpenCV Bridge]<br />
<br />
Once the library is available, in C++ you can include header files and use the video IO factory through ITK to read from file:<br />
<br />
itk::VideoIOBase::Pointer ioReadFile = itk::VideoIOFactory::CreateVideoIO(<br />
itk::VideoIOFactory::ReadFileMode, input);<br />
if (!ioReadFile)<br />
{<br />
std::cerr << "Did not create valid VideoIO for reading from file " << std::endl;<br />
return;<br />
}<br />
<br />
You can also use the OpenCV library directly to access an attached camera:<br />
<br />
itk::SizeValueType cameraNumber = 0;<br />
CvCapture* cameraCapture = cvCaptureFromCAM( cameraNumber );<br />
if (cameraCapture == ITK_NULLPTR)<br />
{<br />
std::cerr << "Unable to create a camera to capture from" << std::endl;<br />
return;<br />
}<br />
}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/ModulesMetadata&diff=45220Documentation/Nightly/ModulesMetadata2016-04-22T22:40:58Z<p>Nicole: Update link to Models documentation xml file</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<includeonly><br />
Name, XMLDescriptionURL<br />
ACPCTransform, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ACPCTransform/ACPCTransform.xml?revision=22697&view=co<br />
AddScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/AddScalarVolumes/AddScalarVolumes.xml?revision=19194&view=co<br />
AffineRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/AffineRegistration/AffineRegistration.xml?revision=19194&view=co<br />
Annotations, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Annotations/Documentation/Annotations.xml?revision=22424&view=co<br />
BRAINSDemonWarp, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSDemonWarp/BRAINSDemonWarp.xml<br />
BRAINSFit, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSFit/BRAINSFit.xml<br />
BRAINSResample, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSResample/BRAINSResample.xml<br />
BSplineDeformableRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/BSplineDeformableRegistration/BSplineDeformableRegistration.xml?revision=19194&view=co<br />
BSplineToDeformationField, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/BSplineToDeformationField/BSplineToDeformationField.xml?revision=19194&view=co<br />
Cameras, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Core/Cameras/Documentation/Cameras.xml?revision=19238&view=co<br />
CastScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CastScalarVolume/CastScalarVolume.xml?revision=19608&view=co<br />
CheckerBoardFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CheckerBoardFilter/CheckerBoardFilter.xml?revision=19170&view=co<br />
CLIModuleTemplate, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.xml?revision=22715&view=co<br />
CreateDICOMSeries, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CreateDICOMSeries/CreateDICOMSeries.xml?revision=19171&view=co<br />
CurvatureAnisotropicDiffusion, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CurvatureAnisotropicDiffusion/CurvatureAnisotropicDiffusion.xml?revision=18864&view=co<br />
Data, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Data/Documentation/Data.xml?revision=22613&view=co<br />
DICOM, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/DICOM.xml?revision=19903&view=co<br />
DicomToNrrdConverter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DicomToNrrdConverter/DicomToNrrdConverter.xml?revision=19089&view=co<br />
DiffusionTensorScalarMeasurements, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DiffusionTensorScalarMeasurements/DiffusionTensorScalarMeasurements.xml?revision=19172&view=co<br />
DiffusionWeightedVolumeMasking, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DiffusionWeightedVolumeMasking/DiffusionWeightedVolumeMasking.xml?revision=19194&view=co<br />
DTIExport, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DTIImportExport/DTIexport.xml?revision=19928&view=co<br />
DTIImport, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DTIImportExport/DTIimport.xml?revision=19928&view=co<br />
DWICompare, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DicomToNrrdConverter/ExtendedTesting/DWICompare.xml?revision=18864&view=co<br />
DWIConverter, https://raw.githubusercontent.com/BRAINSia/BRAINSTools/487208d64667a95ece1a4e4a6aa1f19273108d18/DWIConvert/DWIConvert.xml<br />
DWModeling, https://raw.githubusercontent.com/SlicerProstate/SlicerProstate/master/DWModeling/DWModeling.xml<br />
DWIJointRicianLMMSEFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIJointRicianLMMSEFilter/DWIJointRicianLMMSEFilter.xml?revision=19197&view=co<br />
DWIRicianLMMSEFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIRicianLMMSEFilter/DWIRicianLMMSEFilter.xml?revision=19197&view=co<br />
DWIToDTIEstimation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIToDTIEstimation/DWIToDTIEstimation.xml?revision=19201&view=co<br />
DWIUnbiasedNonLocalMeansFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIUnbiasedNonLocalMeansFilter/DWIUnbiasedNonLocalMeansFilter.xml?revision=19197&view=co<br />
EncodeSEG, https://raw.githubusercontent.com/QIICR/Reporting/master/SEGSupport/EncodeSEG.xml<br />
EMSegment_Command-line, http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co<br />
Endoscopy, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/Endoscopy.xml?revision=18864&view=co<br />
EventBroker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Core/EventBroker/Documentation/EventBroker.xml?revision=19045&view=co<br />
ExecutionModelTour, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExecutionModelTour/ExecutionModelTour.xml?revision=19194&view=co<br />
ExpertAutomatedRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExpertAutomatedRegistration/ExpertAutomatedRegistration.xml?revision=19173&view=co<br />
ExtractSkeleton, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExtractSkeleton/ExtractSkeleton.xml?revision=18864&view=co<br />
FiberBundleLabelSelection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FiberBundleLabelSelect/FiberBundleLabelSelect.xml?view=co&content-type=text%2Fplain<br />
FiducialRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FiducialRegistration/FiducialRegistration.xml?revision=19173&view=co<br />
ForegroundMasking, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSROIAuto/BRAINSROIAuto.xml<br />
FreesurferSurfaceSectionExtraction, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FreesurferSurfaceSectionExtraction/FreesurferSurfaceSectionExtraction.xml?revision=18864&view=co<br />
GaussianBlurImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GaussianBlurImageFilter/GaussianBlurImageFilter.xml?revision=19194&view=co<br />
GradientAnisotropicDiffusion, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GradientAnisotropicDiffusion/GradientAnisotropicDiffusion.xml?revision=18864&view=co<br />
GrayscaleFillHoleImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleFillHoleImageFilter/GrayscaleFillHoleImageFilter.xml?revision=19194&view=co<br />
GrayscaleGrindPeakImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleGrindPeakImageFilter/GrayscaleGrindPeakImageFilter.xml?revision=19194&view=co<br />
GrayscaleModelMaker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.xml?revision=18864&view=co<br />
HistogramMatching, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/HistogramMatching/HistogramMatching.xml?revision=18864&view=co<br />
ImageLabelCombine, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ImageLabelCombine/ImageLabelCombine.xml?revision=18864&view=co<br />
LabelMapSmoothing, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/LabelMapSmoothing/LabelMapSmoothing.xml?revision=18864&view=co<br />
LinearRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/LinearRegistration/LinearRegistration.xml?revision=19194&view=co<br />
Markups, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Markups/Documentation/Markups.xml?revision=23878&view=co<br />
MaskScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MaskScalarVolume/MaskScalarVolume.xml?revision=19608&view=co<br />
MatlabCommander, https://www.assembla.com/code/slicerrt/subversion/node/blob/trunk/MatlabBridge/src/MatlabCommander/MatlabCommander.xml?raw=1&rev=957<br />
MedianImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MedianImageFilter/MedianImageFilter.xml?revision=19194&view=co<br />
MergeModels, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MergeModels/MergeModels.xml?revision=22697&view=co<br />
MeshContourSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MeshContourSegmentation/MeshContourSegmentation.xml?revision=19175&view=co<br />
ModelMaker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ModelMaker/ModelMaker.xml?revision=22697&view=co<br />
Models, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Models/Documentation/Models.xml?revision=25018&view=co<br />
ModelToLabelMap, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ModelToLabelMap/ModelToLabelMap.xml?revision=22697&view=co<br />
MRIBiasFieldCorrection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MRIBiasFieldCorrection/MRIBiasFieldCorrection.xml?revision=18864&view=co<br />
MultiplyScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MultiplyScalarVolumes/MultiplyScalarVolumes.xml?revision=19194&view=co<br />
MultiResolutionAffineRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MultiResolutionAffineRegistration/MultiResolutionAffineRegistration.xml?revision=19194&view=co<br />
N4ITKBiasFieldCorrection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/N4ITKBiasFieldCorrection/N4ITKBiasFieldCorrection.xml?revision=22688&view=co<br />
OrientScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OrientScalarVolume/OrientScalarVolume.xml?revision=19193&view=co<br />
OtsuThresholdImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OtsuThresholdImageFilter/OtsuThresholdImageFilter.xml?revision=19194&view=co<br />
OtsuThresholdSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OtsuThresholdSegmentation/OtsuThresholdSegmentation.xml?revision=18864&view=co<br />
PETStandardUptakeValueComputation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/PETStandardUptakeValueComputation/PETStandardUptakeValueComputation.xml?revision=19608&view=co<br />
PkModeling, https://raw.githubusercontent.com/millerjv/PkModeling/master/CLI/PkModeling.xml<br />
ProbeVolumeWithModel, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ProbeVolumeWithModel/ProbeVolumeWithModel.xml?revision=19194&view=co<br />
QuadEdgeSurfaceMesher, https://raw.githubusercontent.com/SlicerProstate/SlicerProstate/master/QuadEdgeSurfaceMesher/QuadEdgeSurfaceMesher.xml<br />
Reformat, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Reformat/Documentation/Reformat.xml?revision=19165&view=co<br />
ResampleDTIVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleDTIVolume/ResampleDTIVolume.xml?revision=19197&view=co<br />
ResampleScalarVectorDWIVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleScalarVectorDWIVolume/ResampleScalarVectorDWIVolume.xml?revision=19186&view=co<br />
ResampleScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleScalarVolume/ResampleScalarVolume.xml?revision=19185&view=co<br />
RigidRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/RigidRegistration/RigidRegistration.xml?revision=19194&view=co<br />
RobustStatisticsSegmenter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/RobustStatisticsSegmenter/RobustStatisticsSegmenter.xml?revision=19198&view=co<br />
SceneViews, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/SceneViews/Documentation/SceneViews.xml?revision=19608&view=co<br />
SEG2NRRD, https://raw.githubusercontent.com/QIICR/Reporting/master/SEGSupport/SEG2NRRD.xml<br />
SegmentationSmoothing, https://raw.githubusercontent.com/SlicerProstate/SlicerProstate/master/SegmentationSmoothing/SegmentationSmoothing.xml<br />
SimpleRegionGrowingSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/SimpleRegionGrowingSegmentation/SimpleRegionGrowingSegmentation.xml?revision=22482&view=co<br />
SubtractScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/SubtractScalarVolumes/SubtractScalarVolumes.xml?revision=19194&view=co<br />
Tables, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Tables/Documentation/Tables.xml?revision=24790&view=co<br />
ThresholdScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.xml?revision=22407&view=co<br />
TractographyLabelMapSeeding, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.xml?revision=19194&view=co<br />
Transforms, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Transforms/Documentation/Transforms.xml?revision=19899&view=co<br />
ViewControllers, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/ViewControllers/Documentation/ViewControllers.xml?revision=18864&view=co<br />
VolumeRendering, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/VolumeRendering/Documentation/VolumeRendering.xml?revision=22805&view=co<br />
Volumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Volumes/Documentation/Volumes.xml?revision=24213&view=co<br />
VotingBinaryHoleFillingImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/VotingBinaryHoleFillingImageFilter/VotingBinaryHoleFillingImageFilter.xml?revision=19194&view=co<br />
</includeonly><noinclude><br />
<br />
{{ambox<br />
| type = warning<br />
| text = To force MediaWiki to clear the cached version of a given page, or to force the page to be redisplayed from its source.<br> Add '''?action=purge''' to the URL of the page you are viewing. For more details, click [http://www.mediawiki.org/wiki/Manual:Purge here].<br />
}}<br />
<br />
{{#get_web_data:<br />
url={{fullurl:Special:GetData/Documentation/{{documentation/version}}/ModulesMetadata}}<br />
|format=CSV with header|data=name=Name,xmldescriptionurl=XMLDescriptionURL}}<br />
{| class="wikitable sortable"<br />
! Name<br />
! XMLDescriptionURL {{#for_external_table:<nowiki/><br />
{{!}}-<br />
{{!}} {{{name}}}<br />
{{!}} {{{xmldescriptionurl}}} }}<br />
|}<br />
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url={{fullurl:Special:GetData/Documentation/{{documentation/version}}/ModulesMetadata}}<br />
|format=CSV with header<br />
|data=GaussianBlurImageFilterXMLDescriptionURL=XMLDescriptionURL<br />
|filters=Name=GaussianBlurImageFilter<br />
}}<br />
* {{#external_value:GaussianBlurImageFilterXMLDescriptionURL}}<br />
</noinclude></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/OpenCVExample&diff=45171Documentation/Nightly/Extensions/OpenCVExample2016-04-15T16:03:57Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:OpenCVExample.png|x200px]]<br />
<br />
This extension provides an example on how to build and run against the OpenCV package provided by the <br />
[[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV | SlicerOpenCV extension]]. [http://opencv.org/ OpenCV] (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.<br />
<br />
This extension includes a C++ CLI module that loads, operates on, and saves PNG images.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* This module can be used as a template by extension developers who wish to use the algorithms provided by [http://opencv.org OpenCV].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The ExampleOpenCV extension provides the [[Documentation/{{documentation/version}}/Extensions/BlendVectorVolumes|Blend Vector Volumes]] CLI as a stand alone module, but the extension does not provide an overall GUI.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV | SlicerOpenCV extension]].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]<br />
* [http://opencv.org Open Source Computer Vision]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Use this extension as a template on how to include OpenCV provided by the SlicerOpenCV module.<br />
<br />
In your extension's top level CMakeList.txt:<br />
* Specify that it depends on SlicerOpenCV:<br />
set(EXTENSION_DEPENDS "SlicerOpenCV")<br />
* Include the SlicerOpenCV extension by including this line after the find_package for Slicer:<br />
find_package(SlicerOpenCV REQUIRED)<br />
* If you're building from a locally built version of SlicerOpenCV, SlicerOpenCV_DIR is set to the inner-build sub-directory of the SlicerOpenCV build directory.<br />
<br />
In your extension's module CMakeLists.txt file:<br />
* Define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
* The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
* Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
* Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Examples]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BlendVectorVolumes&diff=45159Documentation/Nightly/Extensions/BlendVectorVolumes2016-04-12T16:23:45Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This is a CLI module that depends on the [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV extension]], providing a way to blend two vector volumes together. It uses the OpenCV function [http://docs.opencv.org/3.1.0/d2/de8/group__core__array.html#gafafb2513349db3bcff51f54ee5592a19 addWeighted].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
When loading in RGB files, they are loaded as vector volumes in Slicer. Use this module to blend them together if they have the same dimensions.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
{|<br />
| [[Image:BlendVectorVolumes-GUI.png|thumb|200px|Blend Vector Volumes GUI]]<br />
|<br />
'''IO:'''<br />
* Alpha: A double value between 0.0 and 1.0 that gives the weight of the first input image in the resulting blend.<br />
* Gamma: A double value that is added to the weighted blend, used to increase or decrease intensity.<br />
* First Input Volume: First input vector volume<br />
* Second Input Volume: Second input vector volume, must have the same dimensions as the first input volume.<br />
* Output Volume: Output vector volume, holding the blending of the two input volumes, Can be a newly created vector volume.<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV extension]]. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]<br />
* [http://opencv.org Open Source Computer Vision]<br />
** [http://docs.opencv.org/3.1.0/d2/de8/group__core__array.html#gafafb2513349db3bcff51f54ee5592a19 addWeighted] documentation for version 3.1<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
To depend on the OpenCV provided by the [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]] extension, in the CLI's CMakeLists.txt file define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
* The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
* Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
* Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
[[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]] provides some more information about writing an extension that includes modules that depend on OpenCV<br />
<br />
The images are read in using the opencv imread method. The blending is done by the opencv addWeighted function, and the output is written using imwrite.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Filtering]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/ModuleExtensionListing/Extensions_by_category&diff=45156Documentation/Nightly/ModuleExtensionListing/Extensions by category2016-04-11T21:37:56Z<p>Nicole: /* Extensions by category */</p>
<hr />
<div>__NOTOC__<br />
* [[#Extensions_by_category|Extensions by category]]<br />
= Extensions by category =<br />
24 categories:<br />
* [[#Extensions_by_category_Cardiac|Cardiac]]<br />
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]<br />
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]<br />
* [[#Extensions_by_category_Converters|Converters]]<br />
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]<br />
* [[#Extensions_by_category_Diffusion|Diffusion]]<br />
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]<br />
* [[#Extensions_by_category_Examples|Examples]]<br />
* [[#Extensions_by_category_Exporter|Exporter]]<br />
* [[#Extensions_by_category_Filtering|Filtering]]<br />
* [[#Extensions_by_category_IGT|IGT]]<br />
* [[#Extensions_by_category_Informatics|Informatics]]<br />
* [[#Extensions_by_category_Libraries|Libraries]]<br />
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]<br />
* [[#Extensions_by_category_Microscopy|Microscopy]]<br />
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]<br />
* [[#Extensions_by_category_Quantification|Quantification]]<br />
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]<br />
* [[#Extensions_by_category_Registration|Registration]]<br />
* [[#Extensions_by_category_Scoliosis|Scoliosis]]<br />
* [[#Extensions_by_category_Segmentation|Segmentation]]<br />
* [[#Extensions_by_category_Sequences|Sequences]]<br />
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]<br />
* [[#Extensions_by_category_Tractography|Tractography]]<br />
* [[#Extensions_by_category_Training|Training]]<br />
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]<br />
* [[#Extensions_by_category_Wizards|Wizards]]<br />
<span id='Extensions_by_category_Cardiac'></span><br />
== Cardiac ==<br />
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]<br />
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]<br />
<span id='Extensions_by_category_Cardiac_MRI_toolkit'></span><br />
== Cardiac MRI toolkit ==<br />
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]<br />
<span id='Extensions_by_category_Chest_Imaging_Platform'></span><br />
== Chest Imaging Platform ==<br />
* [http://www.chestimagingplatform.org Chest Imaging Platform]<br />
<span id='Extensions_by_category_Converters'></span><br />
== Converters ==<br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]<br />
<span id='Extensions_by_category_Developer_Tools'></span><br />
== Developer Tools ==<br />
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]<br />
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]<br />
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]<br />
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]<br />
<span id='Extensions_by_category_Diffusion'></span><br />
== Diffusion ==<br />
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]<br />
<span id='Extensions_by_category_Editor_Effects'></span><br />
== Editor Effects ==<br />
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]<br />
<span id='Extensions_by_category_Exporter'></span><br />
== Examples ==<br />
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]<br />
<span id='Extensions_by_category_Examples'></span><br />
== Exporter ==<br />
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]<br />
<span id='Extensions_by_category_IGT'></span><br />
== Filtering ==<br />
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]<br />
<span id='Extensions_by_category_Filtering'></span><br />
== IGT ==<br />
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]<br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]<br />
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]<br />
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]<br />
* [https://github.com/SlicerIGT/LumpNav Lump Nav]<br />
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]<br />
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]<br />
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]<br />
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]<br />
<span id='Extensions_by_category_Informatics'></span><br />
== Informatics ==<br />
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]<br />
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]<br />
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]<br />
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]<br />
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]<br />
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]<br />
<span id='Extensions_by_category_Mesh_Generation'></span><br />
== Libraries ==<br />
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]<br />
<span id='Extensions_by_category_Libraries'></span><br />
== Mesh Generation ==<br />
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]<br />
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]<br />
<span id='Extensions_by_category_Microscopy'></span><br />
== Microscopy ==<br />
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]<br />
<span id='Extensions_by_category_Nuclear_Medicine'></span><br />
== Nuclear Medicine ==<br />
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]<br />
<span id='Extensions_by_category_Quantification'></span><br />
== Quantification ==<br />
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]<br />
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]<br />
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]<br />
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]<br />
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]<br />
<span id='Extensions_by_category_Radiotherapy'></span><br />
== Radiotherapy ==<br />
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]<br />
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]<br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]<br />
<span id='Extensions_by_category_Registration'></span><br />
== Registration ==<br />
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]<br />
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]<br />
<span id='Extensions_by_category_Scoliosis'></span><br />
== Scoliosis ==<br />
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]<br />
<span id='Extensions_by_category_Segmentation'></span><br />
== Segmentation ==<br />
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]<br />
* [http://www.nitrc.org/projects/abc ABC]<br />
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]<br />
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]<br />
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]<br />
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]<br />
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]<br />
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]<br />
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]<br />
* [https://github.com/Tomnl/Slicer-Wasp Wasp]<br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]<br />
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]<br />
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]<br />
<span id='Extensions_by_category_Sequences'></span><br />
== Sequences ==<br />
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]<br />
<span id='Extensions_by_category_Shape_Analysis'></span><br />
== Shape Analysis ==<br />
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]<br />
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]<br />
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]<br />
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]<br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]<br />
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]<br />
<span id='Extensions_by_category_Tractography'></span><br />
== Tractography ==<br />
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]<br />
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]<br />
<span id='Extensions_by_category_Training'></span><br />
== Training ==<br />
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]<br />
<span id='Extensions_by_category_Vascular_Modeling_Toolkit'></span><br />
== Vascular Modeling Toolkit ==<br />
* [http://slicer.vmtk.org/ VMTK]<br />
<span id='Extensions_by_category_Wizards'></span><br />
== Wizards ==<br />
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]<br />
__NOTOC__</div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BlendVectorVolumes&diff=45155Documentation/Nightly/Extensions/BlendVectorVolumes2016-04-11T21:22:46Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This is a CLI module that depends on the [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV extension]], providing a way to blend two vector volumes together.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
When loading in RGB files, they are loaded as vector volumes in Slicer. Use this module to blend them together if they have the same dimensions.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
{|<br />
| [[Image:BlendVectorVolumes-GUI.png|thumb|200px|Blend Vector Volumes GUI]]<br />
|<br />
'''IO:'''<br />
* Alpha: A double value between 0.0 and 1.0 that gives the weight of the first input image in the resulting blend.<br />
* Gamma: A double value that is added to the weighted blend, used to increase or decrease intensity.<br />
* First Input Volume: First input vector volume<br />
* Second Input Volume: Second input vector volume, must have the same dimensions as the first input volume.<br />
* Output Volume: Output vector volume, holding the blending of the two input volumes, Can be a newly created vector volume.<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV extension]]. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]<br />
* [http://opencv.org Open Source Computer Vision]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
To depend on the OpenCV provided by the [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]] extension, in the CLI's CMakeLists.txt file define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
* The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
* Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
* Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
[[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]] provides some more information about writing an extension that includes modules that depend on OpenCV<br />
<br />
The images are read in using the opencv imread method. The blending is done by the opencv addWeighted function, and the output is written using imwrite.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Filtering]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/OpenCVExample&diff=45154Documentation/Nightly/Extensions/OpenCVExample2016-04-11T19:58:49Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:OpenCVExample.png|x200px]]<br />
<br />
This extension provides an example on how to build and run against the OpenCV package provided by the <br />
[[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV | SlicerOpenCV extension]]. [http://opencv.org/ OpenCV] (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.<br />
<br />
This extension includes a C++ CLI module that loads, operates on, and saves PNG images.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* This module can be used as a template by extension developers who wish to use the algorithms provided by [http://opencv.org OpenCV].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The ExampleOpenCV extension provides the [[Documentation/{{documentation/version}}/Extensions/BlendVectorVolumes|Blend Vector Volumes]] CLI as a stand alone module, but the extension does not provide an overall GUI.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV | SlicerOpenCV extension]].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]<br />
* [http://opencv.org Open Source Computer Vision]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Use this extension as a template on how to include OpenCV provided by the SlicerOpenCV module:<br />
* In your extension's top level CMakeList.txt:<br />
** Specify that it depends on SlicerOpenCV:<br />
set(EXTENSION_DEPENDS "SlicerOpenCV")<br />
** Include the SlicerOpenCV extension by including this line after the find_package for Slicer:<br />
find_package(SlicerOpenCV REQUIRED)<br />
* In your extension's module CMakeLists.txt file:<br />
** Define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
** The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
** Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
** Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Examples]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/OpenCVExample&diff=45153Documentation/Nightly/Extensions/OpenCVExample2016-04-11T19:56:32Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
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{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:OpenCVExample.png|x200px]]<br />
<br />
This extension provides an example on how to build and run against the OpenCV package provided by the <br />
[[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV | SlicerOpenCV extension]]. It includes a C++ CLI module that loads, operates on, and saves PNG images.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* This module can be used as a template by extension developers who wish to use the algorithms provided by [http://opencv.org OpenCV].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The ExampleOpenCV extension provides the [[Documentation/{{documentation/version}}/Extensions/BlendVectorVolumes|Blend Vector Volumes]] CLI as a stand alone module, but the extension does not provide an overall GUI.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]<br />
* [http://opencv.org Open Source Computer Vision]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Use this extension as a template on how to include OpenCV provided by the SlicerOpenCV module:<br />
* In your extension's top level CMakeList.txt:<br />
** Specify that it depends on SlicerOpenCV:<br />
set(EXTENSION_DEPENDS "SlicerOpenCV")<br />
** Include the SlicerOpenCV extension by including this line after the find_package for Slicer:<br />
find_package(SlicerOpenCV REQUIRED)<br />
* In your extension's module CMakeLists.txt file:<br />
** Define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
** The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
** Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
** Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Examples]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerOpenCV&diff=45152Documentation/Nightly/Extensions/SlicerOpenCV2016-04-11T19:50:14Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contributor1: Andrey Fedorov ({{collaborator|name|spl}})<br><br />
Contributor2: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:SlicerOpenCV-logo.png|x200px]]<br />
<br />
This extension provides a way for a Slicer extension developer to build against the OpenCV pacakge, by depending on the SlicerOpenCV extension. <br />
[http://opencv.org OpenCV] (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* If an extension developer needs the algorithms provided by OpenCV, they can add a module dependency on SlicerOpenCV and obtain a Slicer style library to link against and use.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The OpenCV module doesn't provide a GUI, it's intended to be used at the library level by other modules.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
* The [[Documentation/{{documentation/version}}/Extensions/OpenCVExample | OpenCVExample]] extension depends on this module and provides a template for linking and using OpenCV.<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]<br />
* [http://opencv.org Open Source Computer Vision] <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
* Include the SlicerOpenCV extension by calling find_package(SlicerOpenCV REQUIRED). This will set OpenCV_DIR in the scope of your extension.<br />
* This extension also provides the ITK module Video Bridge OpenCV [http://insightsoftwareconsortium.github.io/ITKBarCamp-doc/ITK/VideoProcessingUsingOpenCVBridge/index.html Video Processing Using OpenCV Bridge]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BlendVectorVolumes&diff=45118Documentation/Nightly/Extensions/BlendVectorVolumes2016-04-01T21:10:42Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This is a CLI module that depends on the SlicerOpenCV extension, providing a way to blend two vector volumes together.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
When loading in RGB files, they are loaded as vector volumes in Slicer. Use this module to blend them together if they have the same dimensions.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
{|<br />
| [[Image:BlendVectorVolumes-GUI.png|thumb|200px|Blend Vector Volumes GUI]]<br />
|<br />
'''IO:'''<br />
* Alpha: A double value between 0.0 and 1.0 that gives the weight of the first input image in the resulting blend.<br />
* Gamma: A double value that is added to the weighted blend, used to increase or decrease intensity.<br />
* First Input Volume: First input vector volume<br />
* Second Input Volume: Second input vector volume, must have the same dimensions as the first input volume.<br />
* Output Volume: Output vector volume, holding the blending of the two input volumes, Can be a newly created vector volume.<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Quantitative Image Informatics for Cancer Research (QIICR) http://qiicr.org<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
To depend on the OpenCV provided by SlicerOpenCV, in the CLI's CMakeLists.txt file define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
* The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
* Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
* Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
[[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]] provides some more information about writing an extension that includes modules that depend on OpenCV<br />
<br />
The images are read in using the opencv imread method. The blending is done by the opencv addWeighted function, and the output is written using imwrite.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Filtering]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BlendVectorVolumes&diff=45117Documentation/Nightly/Extensions/BlendVectorVolumes2016-04-01T20:44:40Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This is a CLI module that depends on the SlicerOpenCV extension, providing a way to blend two vector volumes together.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
When loading in RGB files, they are loaded as vector volumes in Slicer. Use this module to blend them together.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
{|<br />
| [[Image:BlendVectorVolumes-GUI.png|thumb|200px|Blend Vector Volumes GUI]]<br />
|<br />
'''IO:'''<br />
* Alpha: A double value between 0.0 and 1.0 that gives the weight of the first input image in the resulting blend.<br />
* Gamma: A double value that is added to the weighted blend, used to increase or decrease intensity.<br />
* First Input Volume: First input vector volume<br />
* Second Input Volume: Second input vector volume<br />
* Output Volume: Output vector volume, holding the blending of the two input volumes, Can be a newly created vector volume.<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Quantitative Image Informatics for Cancer Research (QIICR) http://qiicr.org<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
To depend on the OpenCV provided by SlicerOpenCV, in the CLI's CMakeLists.txt file define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
* The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
* Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
* Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
[[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]] provides some more information about writing an extension that includes modules that depend on OpenCV<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Filtering]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=File:BlendVectorVolumes-GUI.png&diff=45116File:BlendVectorVolumes-GUI.png2016-04-01T20:34:09Z<p>Nicole: </p>
<hr />
<div></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/OpenCVExample&diff=45115Documentation/Nightly/Extensions/OpenCVExample2016-04-01T19:30:05Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:OpenCVExample.png|x200px]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
This extension provides an example on how to build and run against the OpenCV package provided by the SlicerOpenCV extension.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The ExampleOpenCV extension provides the [[Documentation/{{documentation/version}}/Extensions/BlendVectorVolumes|Blend Vector Volumes]] CLI as a stand alone module, but the extension does not provide an overall GUI.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Quantitative Image Informatics for Cancer Research (QIICR) http://qiicr.org<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Use this extension as a template on how to include OpenCV provided by the SlicerOpenCV module:<br />
* In your extension's top level CMakeList.txt:<br />
** Specify that it depends on SlicerOpenCV:<br />
set(EXTENSION_DEPENDS "SlicerOpenCV")<br />
** Include the SlicerOpenCV extension by including this line after the find_package for Slicer:<br />
find_package(SlicerOpenCV REQUIRED)<br />
* In your extension's module CMakeLists.txt file:<br />
** Define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
** The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
** Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
** Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Examples]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/BlendVectorVolumes&diff=45114Documentation/Nightly/Extensions/BlendVectorVolumes2016-04-01T19:28:27Z<p>Nicole: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This is a CLI module that depends on the SlicerOpenCV extension, providing a way to blend two vector volumes together.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
When loading in RGB files, they are loaded as vector volumes in Slicer. Use this module to blend them together.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
* Alpha: A double value between 0.0 and 1.0 that gives the weight of the first input image in the resulting blend.<br />
* Gamma: A double value that is added to the weighted blend, used to increase or decrease intensity.<br />
* First Input Volume: First input vector volume<br />
* Second Input Volume: Second input vector volume<br />
* Output Volume: Output vector volume, holding the blending of the two inputs<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Quantitative Image Informatics for Cancer Research (QIICR) http://qiicr.org<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
To depend on the OpenCV provided by SlicerOpenCV, in the CLI's CMakeLists.txt file define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
* The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
* Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
* Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
[[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]] provides some more information about writing an extension that includes modules that depend on OpenCV<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Filtering]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/OpenCVExample&diff=45113Documentation/Nightly/Extensions/OpenCVExample2016-04-01T19:25:44Z<p>Nicole: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/OpenCVExample|OpenCVExample]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:OpenCVExample.png|x200px]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
This extension provides an example on how to build and run against the OpenCV package provided by the SlicerOpenCV extension.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The ExampleOpenCV extension provides the [[Documentation/Nightly/Extensions/BlendVectorVolumes|Blend Vector Volumes] CLI as a stand alone module, but the extension does not provide an overall GUI.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension also uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Quantitative Image Informatics for Cancer Research (QIICR) http://qiicr.org<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
Use this extension as a template on how to include OpenCV provided by the SlicerOpenCV module:<br />
* In your extension's top level CMakeList.txt:<br />
** Specify that it depends on SlicerOpenCV:<br />
set(EXTENSION_DEPENDS "SlicerOpenCV")<br />
** Include the SlicerOpenCV extension by including this line after the find_package for Slicer:<br />
find_package(SlicerOpenCV REQUIRED)<br />
* In your extension's module CMakeLists.txt file:<br />
** Define OpenCV_DIR by finding the package that SlicerOpenCV provided:<br />
find_package(OpenCV 3.1 REQUIRED)<br />
** The header include path is defined as:<br />
get_filename_component(OpenCV_INCLUDE_DIR ${OpenCV_DIR}/../../include ABSOLUTE)<br />
** Add ${OpenCV_INCLUDE_DIR} to the MODULE_INCLUDE_DIRECTORIES list<br />
** Link against the OpenCV libraries by adding ${OpenCV_LIBS} to the MODULE_TARGET_LIBRARIES<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Examples]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=File:OpenCVExample.png&diff=45111File:OpenCVExample.png2016-04-01T18:52:33Z<p>Nicole: Icon for the OpenCVExample extension.</p>
<hr />
<div>Icon for the OpenCVExample extension.</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20160321&diff=45094Developer Meetings/201603212016-03-22T14:23:02Z<p>Nicole: </p>
<hr />
<div>= March 22, 2016 =<br />
<br />
= To Discuss=<br />
* Patch release plans<br />
* Stanford meeting<br />
<br />
= Updates =<br />
<br />
= Conclusion =</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/OrganizerInstruction&diff=45093Developer Meetings/OrganizerInstruction2016-03-22T14:18:45Z<p>Nicole: /* Around 4pm, create an event in the "Slicer BarCamp" community and send a first email on the slicer-developer list */</p>
<hr />
<div>__TOC__<br />
<br />
== Hangouts are held every week at 10am on Tuesday mornings ==<br />
<br />
== Day before the hangout, edit Developer meetings page ==<br />
<br />
The day before the hangout, [{{fullurl:Developer_Meetings|action=edit&section=1}} edit] the Developer Meeting page available on the wiki:<br />
<br />
* Uncomment the entry associated with the following week or create the corresponding page.<br />
<br />
<br />
== Around 4pm, create an event in the "Slicer BarCamp" community and send a first email on the slicer-developer list ==<br />
<br />
<br />
After opening the [https://plus.google.com/u/0/communities/105715968666294296532 Slicer BarCamp] page, follow the step described below.<br />
<br />
<gallery widths=550px heights=400px perrow=2><br />
File:SlicerBarCamp-CreateEvent-1.png|Create an event<br />
File:SlicerBarCamp-CreateEvent-2.png|Set event properties<br>(1)Select theme<br>(2)Set hangout name to <code>Developer Hangout</code><br>(3)Set start time (10am)<br>(4)Set end time (11am)<br>(5)Choose "Google hangout" in advanced property<br>(6)Copy link to the wiki page<br>(7)Click on "Invite"<br />
</gallery><br />
<br />
<br />
<!--<br />
Then send an email to the list using the following Email template:<br />
<br />
<pre><br />
Hi Slicers, <br />
<br />
We'll be having our Slicer4 developer hangout tomorrow at 10am EST. Since the Google hangout platform have been upgraded, you will RECEIVE THE LINK allowing to join the hangout FIVE MINUTES BEFORE IT STARTS.<br />
<br />
If you have specific point you want to discuss, consider updating the wiki:<br />
<br />
http://www.slicer.org/slicerWiki/index.php/Developer_Meetings/HANGOUTDATE<br />
</pre><br />
<br />
== Around 9:50am, start a hangout ==<br />
<br />
See Google help: [https://support.google.com/plus/bin/answer.py?hl=en&answer=1215275 Start a hangout] for details<br />
<br />
I usually invite the Slicer Developers circle I created.<br />
<br />
<br />
== Around 9:55am, reply to your first email with hangout link ==<br />
<br />
Email template:<br />
<br />
<pre><br />
The link to access today's hangout will be: https://plus.google.com/hangouts/YOUR-HANGHOUT-LINK<br />
<br />
Talk to you soon, <br />
<br />
Jc<br />
</pre><br />
<br />
--><br />
<br />
== After or during the meeting, update conclusion ==<br />
<br />
After the meeting, update the conclusion and send an email to the slicer developer list.<br />
<br />
See [http://www.slicer.org/slicerWiki/index.php/Developer_Meetings/20120522#Conclusion here] for an example of conclusion and [http://slicer-devel.65872.n3.nabble.com/Slicer-4-hangouts-TODAY-4pm-EDT-tp3971413p4007808.html here] for an example of email.</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/OrganizerInstruction&diff=45092Developer Meetings/OrganizerInstruction2016-03-22T14:17:37Z<p>Nicole: </p>
<hr />
<div>__TOC__<br />
<br />
== Hangouts are held every week at 10am on Tuesday mornings ==<br />
<br />
== Day before the hangout, edit Developer meetings page ==<br />
<br />
The day before the hangout, [{{fullurl:Developer_Meetings|action=edit&section=1}} edit] the Developer Meeting page available on the wiki:<br />
<br />
* Uncomment the entry associated with the following week or create the corresponding page.<br />
<br />
<br />
== Around 4pmm, create an event in the "Slicer BarCamp" community and send a first email on the slicer-developer list ==<br />
<br />
<br />
After opening the [https://plus.google.com/u/0/communities/105715968666294296532 Slicer BarCamp] page, follow the step described below.<br />
<br />
<gallery widths=550px heights=400px perrow=2><br />
File:SlicerBarCamp-CreateEvent-1.png|Create an event<br />
File:SlicerBarCamp-CreateEvent-2.png|Set event properties<br>(1)Select theme<br>(2)Set hangout name to <code>Developer Hangout</code><br>(3)Set start time (10am)<br>(4)Set end time (11am)<br>(5)Choose "Google hangout" in advanced property<br>(6)Copy link to the wiki page<br>(7)Click on "Invite"<br />
</gallery><br />
<br />
<br />
<!--<br />
Then send an email to the list using the following Email template:<br />
<br />
<pre><br />
Hi Slicers, <br />
<br />
We'll be having our Slicer4 developer hangout tomorrow at 10am EST. Since the Google hangout platform have been upgraded, you will RECEIVE THE LINK allowing to join the hangout FIVE MINUTES BEFORE IT STARTS.<br />
<br />
If you have specific point you want to discuss, consider updating the wiki:<br />
<br />
http://www.slicer.org/slicerWiki/index.php/Developer_Meetings/HANGOUTDATE<br />
</pre><br />
<br />
== Around 9:50am, start a hangout ==<br />
<br />
See Google help: [https://support.google.com/plus/bin/answer.py?hl=en&answer=1215275 Start a hangout] for details<br />
<br />
I usually invite the Slicer Developers circle I created.<br />
<br />
<br />
== Around 9:55am, reply to your first email with hangout link ==<br />
<br />
Email template:<br />
<br />
<pre><br />
The link to access today's hangout will be: https://plus.google.com/hangouts/YOUR-HANGHOUT-LINK<br />
<br />
Talk to you soon, <br />
<br />
Jc<br />
</pre><br />
<br />
--><br />
<br />
== After or during the meeting, update conclusion ==<br />
<br />
After the meeting, update the conclusion and send an email to the slicer developer list.<br />
<br />
See [http://www.slicer.org/slicerWiki/index.php/Developer_Meetings/20120522#Conclusion here] for an example of conclusion and [http://slicer-devel.65872.n3.nabble.com/Slicer-4-hangouts-TODAY-4pm-EDT-tp3971413p4007808.html here] for an example of email.</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20160321&diff=45088Developer Meetings/201603212016-03-22T14:10:18Z<p>Nicole: Nicole moved page SlicerWiki:Developer Meetings/20160321 to Developer Meetings/20160321</p>
<hr />
<div><br />
= To Discuss=<br />
<br />
= Updates =<br />
<br />
= Conclusion =</div>Nicolehttps://www.slicer.org/w/index.php?title=Slicer_Wiki:Developer_Meetings/20160321&diff=45089Slicer Wiki:Developer Meetings/201603212016-03-22T14:10:18Z<p>Nicole: Nicole moved page SlicerWiki:Developer Meetings/20160321 to Developer Meetings/20160321</p>
<hr />
<div>#REDIRECT [[Developer Meetings/20160321]]</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20160321&diff=45086Developer Meetings/201603212016-03-22T14:09:54Z<p>Nicole: Nicole moved page Developer Meetings/20160322 to SlicerWiki:Developer Meetings/20160321: date wrong</p>
<hr />
<div><br />
= To Discuss=<br />
<br />
= Updates =<br />
<br />
= Conclusion =</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20160322&diff=45087Developer Meetings/201603222016-03-22T14:09:54Z<p>Nicole: Nicole moved page Developer Meetings/20160322 to SlicerWiki:Developer Meetings/20160321: date wrong</p>
<hr />
<div>#REDIRECT [[SlicerWiki:Developer Meetings/20160321]]</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings&diff=45085Developer Meetings2016-03-22T14:09:04Z<p>Nicole: </p>
<hr />
<div>__NOTOC__<br />
<br />
<!--<br />
<center>[[File:ScreenShot_GoogleHangout.PNG|300px]]</center><br />
--><br />
<br />
== Introduction ==<br />
The Slicer engineering team is distributed across several locations. Because of this, we use a variety of electronic means for communication. In addition to the twice a year [http://wiki.na-mic.org/Wiki/index.php/Project_Events project weeks], and additional topic oriented meeting, we have a weekly Google hangout. <br />
<br />
These meetings are open to anyone. If you are interested, please join the [https://plus.google.com/u/1/communities/105715968666294296532 3DSlicer BarCamp] community on Google Plus.<br />
<br />
<br><br />
{{mbox<br />
| type = style<br />
| text = <big>Open to everyone - Every Tuesday @ 10am EST on [https://plus.google.com/u/0/communities/105715968666294296532/events 3DSlicer BarCamp] community</big><br />
| image= [[File:smile.png|40px]]<br />
}}<br />
<br><br />
<br />
<br />
<small>[[Developer_Meetings/OrganizerInstruction|How to schedule a hangout ?]]</small><br />
<br><small>[[Documentation/Nightly/FAQ/BarCamp#Moderators:_How_to_approve.2Freject_requests_.3F|Moderators:How to approve/reject requests?]]</small><br />
<br />
== 2016 ==<br />
* [[Developer_Meetings/20160321|March 21th, 2016]]<br />
* [[Developer_Meetings/20160315|March 15th, 2016]]<br />
* [[Developer_Meetings/20160308|March 8th, 2016]]<br />
* [[Developer_Meetings/20160301|March 1st, 2016]]<br />
* [[Developer_Meetings/20160223|February 23th, 2016]]<br />
* [[Developer_Meetings/20160216|February 16th, 2016]]<br />
* [[Developer_Meetings/20160209|February 9th, 2016]]<br />
* [[Developer_Meetings/20160202|February 2nd, 2016]]<br />
* [[Developer_Meetings/20160126|January 26th, 2016]]<br />
* [[Developer_Meetings/20160119|January 19th, 2016]]<br />
* [[Developer_Meetings/20160112|January 12th, 2016]]<br />
* January 5th, 2016 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2016_Winter_Project_Week Winter project week]</small><br />
<br />
== 2015 ==<br />
<br />
* December 29th, 2015 - <small>Canceled - Happy holidays</small><br />
* December 22nd, 2015 - <small>Canceled - Happy holidays</small><br />
* [[Developer_Meetings/20151215|December 15th, 2015]]<br />
* [[Developer_Meetings/20151215|December 15th, 2015]]<br />
* [[Developer_Meetings/20151208|December 8th, 2015]]<br />
* [[Developer_Meetings/20151201|December 1st, 2015]]<br />
* [[Developer_Meetings/20151124|November 24th, 2015]] - <small>KickOff for [http://www.na-mic.org/Wiki/index.php/2016_Winter_Project_Week 2016 Project Week @ Cambridge]</small><br />
* [[Developer_Meetings/20151117|November 17th, 2015]]<br />
* [[Developer_Meetings/20151110|November 10th, 2015]]<br />
* [[Developer_Meetings/20151103|November 3rd, 2015]]<br />
* [[Developer_Meetings/20151027|October 27th, 2015]]<br />
* [[Developer_Meetings/20151020|October 20th, 2015]]<br />
* [[Developer_Meetings/20151013|October 13th, 2015]]<br />
* [[Developer_Meetings/20151006|October 6th, 2015]]<br />
* [[Developer_Meetings/20150929|September 29th, 2015]]<br />
* [[Developer_Meetings/20150922|September 22nd, 2015]]<br />
* [[Developer_Meetings/20150915|September 15th, 2015]]<br />
* [[Developer_Meetings/20150908|September 8th, 2015]]<br />
* [[Developer_Meetings/20150901|September 1st, 2015]]<br />
* [[Developer_Meetings/20150825|August 25th, 2015]]<br />
* [[Developer_Meetings/20150818|August 18th, 2015]]<br />
* [[Developer_Meetings/20150811|August 11th, 2015]]<br />
* [[Developer_Meetings/20150804|August 4th, 2015]]<br />
* [[Developer_Meetings/20150728|July 28th, 2015]]<br />
* [[Developer_Meetings/20150714|July 14th, 2015]]<br />
* [[Developer_Meetings/20150707|July 7th, 2015]]<br />
* June 23rd, 2015 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Summer project week]</small><br />
* [[Developer_Meetings/20150616|June 16th, 2015]]<br />
* [[Developer_Meetings/20150609|June 9th, 2015]]<br />
* [[Developer_Meetings/20150602|June 2nd, 2015]]<br />
* [[Developer_Meetings/20150526|May 26th, 2015]]<br />
* [[Developer_Meetings/20150519|May 19th, 2015]]<br />
* [[Developer_Meetings/20150512|May 12th, 2015]]<br />
* [[Developer_Meetings/20150505|May 5th, 2015]]<br />
* [[Developer_Meetings/20150428|April 28st, 2015]]<br />
* [[Developer_Meetings/20150421|April 21st, 2015]]<br />
* [[Developer_Meetings/20150414|April 14th, 2015]]<br />
* [[Developer_Meetings/20150407|April 7th, 2015]]<br />
* [[Developer_Meetings/20150331|March 31st, 2015]]<br />
* [[Developer_Meetings/20150324|March 24th, 2015]]<br />
* [[Developer_Meetings/20150317|March 17th, 2015]]<br />
* [[Developer_Meetings/20150310|March 10th, 2015]]<br />
* [[Developer_Meetings/20150303|March 3rd, 2015]]<br />
* [[Developer_Meetings/20150224|February 24th, 2015]]<br />
* [[Developer_Meetings/20150224|February 24th, 2015]]<br />
* [[Developer_Meetings/20150217|February 17th, 2015]]<br />
* [[Developer_Meetings/20150210|February 10th, 2015]]<br />
* [[Developer_Meetings/20150203|February 3rd, 2015]]<br />
* [[Developer_Meetings/20150127|January 27th, 2015]]<br />
* [[Developer_Meetings/20150120|January 20th, 2015]]<br />
* [[Developer_Meetings/20150113|January 13th, 2015]]<br />
* January 6th, 2015 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Winter project week]</small><br />
<br />
== 2014 ==<br />
* [[Developer_Meetings/20141230|December 30th, 2014]]<br />
* [[Developer_Meetings/20141223|December 23rd, 2014]]<br />
* [[Developer_Meetings/20141216|December 16th, 2014]]<br />
* [[Developer_Meetings/20141209|December 9th, 2014]]<br />
* [[Developer_Meetings/20141202|December 2nd, 2014]]<br />
* [[Developer_Meetings/20141125|November 25th, 2014]]<br />
* [[Developer_Meetings/20141118|November 18th, 2014]]<br />
* [[Developer_Meetings/20141111|November 11th, 2014]]<br />
* [[Developer_Meetings/20141103|November 3rd, 2014]]<br />
* [[Developer_Meetings/20141029|October 29th, 2014]]<br />
* [[Developer_Meetings/20141021|October 21st, 2014]]<br />
* [[Developer_Meetings/20141014|October 14th, 2014]]<br />
* [[Developer_Meetings/20141007|October 7th, 2014]]<br />
* [[Developer_Meetings/20140930|September 30th, 2014]]<br />
* [[Developer_Meetings/20140923|September 23rd, 2014]]<br />
* [[Developer_Meetings/20140916|September 16th, 2014]]<br />
* [[Developer_Meetings/20140909|September 9th, 2014]]<br />
* [[Developer_Meetings/20140901|September 1st, 2014]]<br />
* [[Developer_Meetings/20140826|August 26th, 2014]]<br />
* [[Developer_Meetings/20140819|August 19th, 2014]]<br />
* [[Developer_Meetings/20140812|August 12th, 2014]]<br />
* [[Developer_Meetings/20140805|August 5th, 2014]]<br />
* [[Developer_Meetings/20140729|July 29th, 2014]]<br />
* [[Developer_Meetings/20140722|July 22nd, 2014]]<br />
* [[Developer_Meetings/20140715-2|July 15th, 2014]] <small>Developer hangout</small><br />
* [[Developer_Meetings/20140715|July 15th, 2014]] <small>Extension Developers - From VTK5 to VTK6 - Q&A- Google Hangout</small><br />
* [[Developer_Meetings/20140701|July 1st, 2014]]<br />
* June 24th, 2014 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week 19th NA-MIC project week]</small><br />
* [[Developer_Meetings/20140617|June 17th, 2014]]<br />
* [[Developer_Meetings/20140610|June 10th, 2014]]<br />
* [[Developer_Meetings/20140603|June 3rd, 2014]]<br />
* [[Developer_Meetings/20140527|May 27th, 2014]]<br />
* [[Developer_Meetings/20140520|May 20th, 2014]]<br />
* [[Developer_Meetings/20140513|May 13th, 2014]]<br />
* May 6th, 2014 - <small>Cancelled - [http://www.commontk.org/index.php/CTK-Hackfest-May-2014 CTK Hackfest in St Louis]</small><br />
* [[Developer_Meetings/20140429|April 29th, 2014]]<br />
* [[Developer_Meetings/20140422|April 22th, 2014]]<br />
* [[Developer_Meetings/20140415|April 15th, 2014]]<br />
* [[Developer_Meetings/20140408|April 8th, 2014]]<br />
* [[Developer_Meetings/20140401|April 1st, 2014]]<br />
* [[Developer_Meetings/20140325|March 25th, 2014]]<br />
* [[Developer_Meetings/20140318|March 18th, 2014]]<br />
* [[Developer_Meetings/20140311|March 11th, 2014]]<br />
* [[Developer_Meetings/2014030607|March 6-7, 2014 (Face to Face in Boston)]]<br />
* [[Developer_Meetings/20140304|March 4th, 2014]]<br />
* [[Developer_Meetings/20140225|February 25th, 2014]]<br />
* [[Developer_Meetings/20140218|February 18th, 2014]]<br />
* [[Developer_Meetings/20140211|February 11th, 2014]]<br />
* [[Developer_Meetings/20140204|February 4th, 2014]]<br />
* [[Developer_Meetings/20140128|January 28th, 2014]]<br />
* [[Developer_Meetings/20140121|January 21st, 2014]]<br />
* [[Developer_Meetings/20140114|January 14th, 2014]]<br />
* January 7th, 2014 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/AHM_2014 AHM in Salt Lake City]</small><br />
<br />
== 2013 ==<br />
* December 31th, 2013 - <small>Cancelled - New year day</small><br />
* December 24th, 2013 - <small>Cancelled - Christmas day</small><br />
* [[Developer_Meetings/20131217|December 17, 2013]]<br />
* [[Developer_Meetings/20131210|December 10, 2013]]<br />
* [[Developer_Meetings/20131203|December 3rd, 2013]]<br />
* [[Developer_Meetings/20131126|November 26th, 2013]]<br />
* [[Developer_Meetings/20131119|November 19th, 2013]]<br />
* [[Developer_Meetings/20131112|November 12th, 2013]]<br />
* [[Developer_Meetings/20131105|November 5th, 2013]]<br />
* [[Developer_Meetings/20131029|October 29th, 2013]]<br />
* [[Developer_Meetings/20131022|October 22th, 2013]]<br />
* [[Developer_Meetings/20131015|October 15th, 2013]]<br />
* [[Developer_Meetings/20131008|October 8th, 2013]]<br />
* [[Developer_Meetings/20131001|October 1st, 2013]]<br />
* [[Developer_Meetings/20130924|September 24th, 2013]]<br />
* [[Developer_Meetings/20130917|September 17th, 2013]]<br />
* [[Developer_Meetings/20130910|September 10th, 2013]]<br />
* [[Developer_Meetings/20130903|September 3rd, 2013]]<br />
* [[Developer_Meetings/20130827|August 27th, 2013]]<br />
* [[Developer_Meetings/20130820|August 20th, 2013]]<br />
* [[Developer_Meetings/20130813|August 13th, 2013]]<br />
* [[Developer_Meetings/20130806|August 6th, 2013]]<br />
* [[Developer_Meetings/20130730|July 30th, 2013]]<br />
* [[Developer_Meetings/20130723|July 23rd, 2013]]<br />
* [[Developer_Meetings/20130716|July 16th, 2013]]<br />
* [[Developer_Meetings/20130709|July 9th, 2013]]<br />
* [[Developer_Meetings/20130702|July 2nd, 2013]]<br />
* June 18th, 23rd 2013 - cancelled due to NA-MIC Project week<br />
* [[Developer_Meetings/20130611|June 11th, 2013]]<br />
* [[Developer_Meetings/20130604|June 4th, 2013]]<br />
* [[Developer_Meetings/20130528|May 28th, 2013]]<br />
* May 21th, 2013 - <small>Cancelled - [http://www.commontk.org/index.php/CTK-Hackfest-May-2013 CTK Hackfest in Canada]</small><br />
* [[Developer_Meetings/20130514|May 14th, 2013]]<br />
* [[Developer_Meetings/20130507|May 7th, 2013]]<br />
* [[Developer_Meetings/20130430|April 30th, 2013]]<br />
* [[Developer_Meetings/20130423|April 23th, 2013]]<br />
* [[Developer_Meetings/20130416|April 16th, 2013]]<br />
* [[Developer_Meetings/20130409|April 9th, 2013]]<br />
* [[Developer_Meetings/20130402|April 2nd, 2013]]<br />
* [[Developer_Meetings/20130326|March 26th, 2013]]<br />
* [[Developer_Meetings/20130319|March 19th, 2013]]<br />
* [[Developer_Meetings/20130312|March 12th, 2013]]<br />
* [[Developer_Meetings/20130305|March 05th, 2013]]<br />
* [[Developer_Meetings/20130226|February 26th, 2013]]<br />
* [[Developer_Meetings/20130219|February 19th, 2013]]<br />
* [[Developer_Meetings/20130212|February 12th, 2013]]<br />
* [[Developer_Meetings/20130205|February 5th, 2013]]<br />
* [[Developer_Meetings/20130129|January 29th, 2013]]<br />
* [[Developer_Meetings/20130122|January 22nd, 2013]]<br />
* January 15th, 2013 - <small>Cancelled - AHM happened previous week</small><br />
* January 8th, 2013 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/AHM_2013 AHM in Salt Lake City]</small><br />
* January 1st, 2013 - <small>Cancelled - New year day</small><br />
<br />
== 2012 ==<br />
* December 25th, 2012 - <small>Cancelled - Christmas day</small><br />
* [[Developer_Meetings/20121218|December 18th, 2012]]<br />
* [[Developer_Meetings/20121211|December 11th, 2012]]<br />
* [[Developer_Meetings/20121204|December 4th, 2012]]<br />
* [[Developer_Meetings/20121127|November 27th, 2012]]<br />
* [[Developer_Meetings/20121120|November 20th, 2012]]<br />
* [[Developer_Meetings/20121113|November 13th, 2012]]<br />
* [[Developer_Meetings/20121106|November 6th, 2012]]<br />
* [[Developer_Meetings/20121030|October 30th, 2012]]<br />
* [[Developer_Meetings/20121023|October 23th, 2012]]<br />
* [[Developer_Meetings/20121016|October 16th, 2012]]<br />
* [[Developer_Meetings/20121009|October 09th, 2012]]<br />
* [[Developer_Meetings/20121002|October 02th, 2012]]<br />
* [[Developer_Meetings/20120925|September 25th, 2012]]<br />
* [[Developer_Meetings/20120918|September 18th, 2012]]<br />
* [[Developer_Meetings/20120911|September 11th, 2012]]<br />
* [[Developer_Meetings/20120904|September 4th, 2012]]<br />
* [[Developer_Meetings/20120828|August 28th, 2012]]<br />
* [[Developer_Meetings/20120821|August 21st, 2012]]<br />
* [[Developer_Meetings/20120814|August 14th, 2012]]<br />
* [[Developer_Meetings/20120807|August 7th, 2012]]<br />
* [[Developer_Meetings/20120731|July 31th, 2012]]<br />
* [[Developer_Meetings/20120724|July 24th, 2012]]<br />
* [[Developer_Meetings/20120717|July 17th, 2012]]<br />
* [[Developer_Meetings/20120710|July 10th, 2012]]<br />
* [[Developer_Meetings/20120703|July 3rd, 2012]]<br />
* [[Developer_Meetings/20120626|June 26th, 2012]]<br />
* [[Developer_Meetings/20120619|June 19th, 2012]]<br />
* [[Developer_Meetings/20120612|June 12th, 2012]]<br />
* [[Developer_Meetings/20120605|June 5th, 2012]]<br />
* [[Developer_Meetings/20120529|May 29, 2012]]<br />
* [[Developer_Meetings/20120522|May 22, 2012]]<br />
* [[Developer_Meetings/20120515|May 15, 2012]]<br />
* [[Developer_Meetings/20120508|May 8, 2012]]<br />
* [[Developer_Meetings/20120501|May 1st, 2012]]<br />
<br />
=== Miscellaneous ===<br />
* [http://wiki.na-mic.org/Wiki/index.php/Slicer4.2Planning August 20st, 2012 - Slicer 4.2 planning]<br />
<br />
== 2010 - 2011 ==<br />
* See [[Slicer4:QtPort/MeetingNotes]]<br />
<br />
== 2009 ==<br />
* September 16-17: [[Slicer:Developer_Meetings:20090916|Slicer widgets brainstorming]] (rough notes)<br />
* February 3: [[Slicer:Developer_Meetings:20090203|mBIRN preparation, Slicer3.4 release]]<br />
<br />
== 2008 ==<br />
* September 16: Demian on Python/Tractography<br />
* August 26: [[Slicer:Developer_Meetings:20080826|Slicer and NA-MIC Overview]]<br />
* August 11: [http://www.na-mic.org/Wiki/index.php/Slicer3_Q%26A_2008-11-18 Introduction of new researchers and developers (17 attendees)]<br />
* July 29: [[Slicer:Developer_Meetings:20080729|Slicer 3.2 release]]<br />
<br />
== 2007 ==<br />
* July 16: [[Slicer:Developer_Meetings:20070716|PNL demo Slicer3]]<br />
* June 12: [[Slicer:Developer_Meetings:20070612|PNL wishlist for Slicer3]]<br />
* March 27: [[Slicer:Developer_Meetings:20070327|Slicer 2.7, Slicer3 beta]]<br />
* February 6: [[Slicer:Developer_Meetings:20070206|Slicer3 mBIRN meeting Prep]]<br />
* January 30: [[Slicer:Developer_Meetings:20070130|Slicer3 Release Planning]]<br />
* January 2: [[Slicer:Developer_Meetings:20070102|Slicer3 AHM Prep]]<br />
<br />
== 2006 ==<br />
* November 21: [[Slicer:Developer_Meetings:20061121|Slicer3 Updates, preparations for retreat]]<br />
* November 07: [[Slicer:Developer_Meetings:20061107|Slicer3 Updates, NA-MIC Mesh Kickoff]]<br />
* October 10: [[Slicer:Developer_Meetings:20061010| Slicer3 Updates]]<br />
* August 29: [[Slicer:Developer_Meetings:20060829|Slicer 3 and Slicer 2.6 bugs]]<br />
* May 2: [[Slicer:Developer_Meetings:20060502|Release 2.6, Fiducials, Slicer for MRT]]<br />
* March 14: [[Slicer:Developer_Meetings:20060314|Release 2.6, mBIRN meeting, Slicer MRT]]<br />
<br />
<br />
== 2005 ==<br />
* June 7: [[Slicer:Developer_Meetings:20050607|NA-MIC Programming Week discussion: Slicer 3]]<br />
* May 24: [[Slicer:Developer_Meetings:20050524|Release 2.5]]<br />
* May 10: [[Slicer:Developer_Meetings:20050510|Release 2.5]]<br />
* April 11: [[Slicer:Developer_Meetings:20050411|To-do list for release 2.5, OpenTracker]]<br />
* March 29: [[Slicer:Developer_Meetings:20050329|Dan Kacher : Integrating trackers with Slicer ]]<br />
* March 15: [[Slicer:Developer_Meetings:20050315|Updates from BIRN Meeting, Training, Windows Building, Release 2.5]]<br />
* March 1: [[Slicer:Developer_Meetings:20050301|Updates from NA-MIC Meeting, Current and Future Projects]]<br />
* February 1: [[Slicer:Developer_Meetings:20050201|Randy Ellis : demo of surgical navigation system]]<br />
* January 18: [[Slicer:Developer_Meetings:20050118|Slicer Architecture]]</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20160321&diff=45084Developer Meetings/201603212016-03-22T14:07:29Z<p>Nicole: Created page with " = To Discuss= = Updates = = Conclusion ="</p>
<hr />
<div><br />
= To Discuss=<br />
<br />
= Updates =<br />
<br />
= Conclusion =</div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerOpenCV&diff=45015Documentation/Nightly/Extensions/SlicerOpenCV2016-03-03T21:33:13Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contributor1: Andrey Fedorov ({{collaborator|name|spl}})<br><br />
Contributor2: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
[[File:SlicerOpenCV-logo.png|x200px]]<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* This extension provides a way for a Slicer extension developer to build against the OpenCV pacakge<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The OpenCV module doesn't provide a GUI, it's intended to be used at the library level by other modules.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Quantitative Image Informatics for Cancer Research (QIICR) http://qiicr.org<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
* Include the SlicerOpenCV extension by calling find_package(SlicerOpenCV REQUIRED). This will set OpenCV_DIR in the scope of your extension.<br />
* This extension also provides the ITK module Video Bridge OpenCV<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=File:SlicerOpenCV-logo.png&diff=45014File:SlicerOpenCV-logo.png2016-03-03T21:30:39Z<p>Nicole: </p>
<hr />
<div></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerOpenCV&diff=45013Documentation/Nightly/Extensions/SlicerOpenCV2016-03-03T20:30:04Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]]<br><br />
Acknowledgments:<br />
This work was supported by a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant U24 CA180918-03 as well as U24 CA180924 Tools to Analyze Morphology and Spatially Mapped Molecular Data with Stony Brook University.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contributor1: Andrey Fedorov ({{collaborator|name|spl}})<br><br />
Contributor2: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* This extension provides a way for a Slicer extension developer to build against the OpenCV pacakge<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The OpenCV module doesn't provide a GUI, it's intended to be used at the library level by other modules.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Quantitative Image Informatics for Cancer Research (QIICR) http://qiicr.org<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
* Include the SlicerOpenCV extension by calling find_package(SlicerOpenCV REQUIRED). This will set OpenCV_DIR in the scope of your extension.<br />
* This extension also provides the ITK module Video Bridge OpenCV<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerOpenCV&diff=45010Documentation/Nightly/Extensions/SlicerOpenCV2016-03-02T20:20:05Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]]<br><br />
Acknowledgments:<br />
This work was done as a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant 5U24CA180918-03.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contributor1: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* This extension provides a way for a Slicer extension developer to build against the OpenCV pacakge<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
The OpenCV module doesn't provide a GUI, it's intended to be used at the library level by other modules.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Quantitative Image Informatics for Cancer Research (QIICR) http://qiicr.org<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
* Include the SlicerOpenCV extension by calling find_package(SlicerOpenCV REQUIRED). This will set OpenCV_DIR in the scope of your extension.<br />
* This extension also provides the ITK module Video Bridge OpenCV<br />
* The [https://github.com/SBU-BMI/SlicerPathology Slicer Pathology] extension uses the SlicerOpenCV extension <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerOpenCV&diff=45009Documentation/Nightly/Extensions/SlicerOpenCV2016-03-02T20:09:49Z<p>Nicole: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]]<br><br />
Acknowledgments:<br />
This work was done as a supplement to the Quantitative Image Informatics project via the NIH-National Cancer Institute Grant 5U24CA180918-03.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contributor1: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* This extension provides a way for a Slicer extension developer to build against the OpenCV pacakge<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
* Include the SlicerOpenCV extension by calling find_package(SlicerOpenCV REQUIRED). This will set OpenCV_DIR in the scope of your extension.<br />
* This extension also provides the ITK module Video Bridge OpenCV<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerOpenCV&diff=45008Documentation/Nightly/Extensions/SlicerOpenCV2016-03-01T23:32:05Z<p>Nicole: Created page with "<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- --------------------..."</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Extension: [[Documentation/{{documentation/version}}/Extensions/SlicerOpenCV|SlicerOpenCV]]<br><br />
Acknowledgments:<br />
This work was done as a supplement to the Quantitative Image Informatics NIH-NCI National Cancer Institute Grant 5U24CA180918-02.<br><br />
Author: Nicole Aucoin ({{collaborator|name|spl}})<br><br />
Contributor1: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
* This extension provides a way for a Slicer extension developer to build against the OpenCV pacakge<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Open Source Computer Vision http://opencv.org<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
* Include the SlicerOpenCV extension by calling find_package(SlicerOpenCV REQUIRED). This will set OpenCV_DIR in the scope of your extension.<br />
* This extension also provides the ITK module Video Bridge OpenCV<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
[[Category:Documentation/{{documentation/version}}/Modules/Libraries]]<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20160202&diff=44810Developer Meetings/201602022016-01-28T20:43:37Z<p>Nicole: Created page with "= Update = * Nicole: SlicerOpenCV = To Discuss= * Template for shared library? = Conclusion ="</p>
<hr />
<div>= Update =<br />
<br />
* Nicole: SlicerOpenCV<br />
<br />
= To Discuss=<br />
<br />
* Template for shared library?<br />
<br />
= Conclusion =</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings&diff=44809Developer Meetings2016-01-28T20:42:27Z<p>Nicole: /* 2016 */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!--<br />
<center>[[File:ScreenShot_GoogleHangout.PNG|300px]]</center><br />
--><br />
<br />
== Introduction ==<br />
The Slicer engineering team is distributed across several locations. Because of this, we use a variety of electronic means for communication. In addition to the twice a year [http://wiki.na-mic.org/Wiki/index.php/Project_Events project weeks], and additional topic oriented meeting, we have a weekly Google hangout meeting every Tuesday @ 2pm EST. <br />
<br />
These meetings are open to anyone. If you are interested, please join the [https://plus.google.com/u/1/communities/105715968666294296532 3DSlicer BarCamp] community on Google Plus.<br />
<br />
<br><br />
{{mbox<br />
| type = style<br />
| text = <big>Open to everyone - Every Tuesday @ 10am EST on [https://plus.google.com/u/0/communities/105715968666294296532/events 3DSlicer BarCamp] community</big><br />
| image= [[File:smile.png|40px]]<br />
}}<br />
<br><br />
<br />
<br />
<small>[[Developer_Meetings/OrganizerInstruction|How to schedule a hangout ?]]</small><br />
<br><small>[[Documentation/Nightly/FAQ/BarCamp#Moderators:_How_to_approve.2Freject_requests_.3F|Moderators:How to approve/reject requests?]]</small><br />
<br />
== 2016 ==<br />
<br />
* [[Developer_Meetings/20160202|February 2nd, 2016]]<br />
* [[Developer_Meetings/20160126|January 26th, 2016]]<br />
* [[Developer_Meetings/20160119|January 19th, 2016]]<br />
* [[Developer_Meetings/20160112|January 12th, 2016]]<br />
* January 5th, 2016 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2016_Winter_Project_Week Winter project week]</small><br />
<br />
== 2015 ==<br />
<br />
* December 29th, 2015 - <small>Canceled - Happy holidays</small><br />
* December 22nd, 2015 - <small>Canceled - Happy holidays</small><br />
* [[Developer_Meetings/20151215|December 15th, 2015]]<br />
* [[Developer_Meetings/20151215|December 15th, 2015]]<br />
* [[Developer_Meetings/20151208|December 8th, 2015]]<br />
* [[Developer_Meetings/20151201|December 1st, 2015]]<br />
* [[Developer_Meetings/20151124|November 24th, 2015]] - <small>KickOff for [http://www.na-mic.org/Wiki/index.php/2016_Winter_Project_Week 2016 Project Week @ Cambridge]</small><br />
* [[Developer_Meetings/20151117|November 17th, 2015]]<br />
* [[Developer_Meetings/20151110|November 10th, 2015]]<br />
* [[Developer_Meetings/20151103|November 3rd, 2015]]<br />
* [[Developer_Meetings/20151027|October 27th, 2015]]<br />
* [[Developer_Meetings/20151020|October 20th, 2015]]<br />
* [[Developer_Meetings/20151013|October 13th, 2015]]<br />
* [[Developer_Meetings/20151006|October 6th, 2015]]<br />
* [[Developer_Meetings/20150929|September 29th, 2015]]<br />
* [[Developer_Meetings/20150922|September 22nd, 2015]]<br />
* [[Developer_Meetings/20150915|September 15th, 2015]]<br />
* [[Developer_Meetings/20150908|September 8th, 2015]]<br />
* [[Developer_Meetings/20150901|September 1st, 2015]]<br />
* [[Developer_Meetings/20150825|August 25th, 2015]]<br />
* [[Developer_Meetings/20150818|August 18th, 2015]]<br />
* [[Developer_Meetings/20150811|August 11th, 2015]]<br />
* [[Developer_Meetings/20150804|August 4th, 2015]]<br />
* [[Developer_Meetings/20150728|July 28th, 2015]]<br />
* [[Developer_Meetings/20150714|July 14th, 2015]]<br />
* [[Developer_Meetings/20150707|July 7th, 2015]]<br />
* June 23rd, 2015 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Summer project week]</small><br />
* [[Developer_Meetings/20150616|June 16th, 2015]]<br />
* [[Developer_Meetings/20150609|June 9th, 2015]]<br />
* [[Developer_Meetings/20150602|June 2nd, 2015]]<br />
* [[Developer_Meetings/20150526|May 26th, 2015]]<br />
* [[Developer_Meetings/20150519|May 19th, 2015]]<br />
* [[Developer_Meetings/20150512|May 12th, 2015]]<br />
* [[Developer_Meetings/20150505|May 5th, 2015]]<br />
* [[Developer_Meetings/20150428|April 28st, 2015]]<br />
* [[Developer_Meetings/20150421|April 21st, 2015]]<br />
* [[Developer_Meetings/20150414|April 14th, 2015]]<br />
* [[Developer_Meetings/20150407|April 7th, 2015]]<br />
* [[Developer_Meetings/20150331|March 31st, 2015]]<br />
* [[Developer_Meetings/20150324|March 24th, 2015]]<br />
* [[Developer_Meetings/20150317|March 17th, 2015]]<br />
* [[Developer_Meetings/20150310|March 10th, 2015]]<br />
* [[Developer_Meetings/20150303|March 3rd, 2015]]<br />
* [[Developer_Meetings/20150224|February 24th, 2015]]<br />
* [[Developer_Meetings/20150224|February 24th, 2015]]<br />
* [[Developer_Meetings/20150217|February 17th, 2015]]<br />
* [[Developer_Meetings/20150210|February 10th, 2015]]<br />
* [[Developer_Meetings/20150203|February 3rd, 2015]]<br />
* [[Developer_Meetings/20150127|January 27th, 2015]]<br />
* [[Developer_Meetings/20150120|January 20th, 2015]]<br />
* [[Developer_Meetings/20150113|January 13th, 2015]]<br />
* January 6th, 2015 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Winter project week]</small><br />
<br />
== 2014 ==<br />
* [[Developer_Meetings/20141230|December 30th, 2014]]<br />
* [[Developer_Meetings/20141223|December 23rd, 2014]]<br />
* [[Developer_Meetings/20141216|December 16th, 2014]]<br />
* [[Developer_Meetings/20141209|December 9th, 2014]]<br />
* [[Developer_Meetings/20141202|December 2nd, 2014]]<br />
* [[Developer_Meetings/20141125|November 25th, 2014]]<br />
* [[Developer_Meetings/20141118|November 18th, 2014]]<br />
* [[Developer_Meetings/20141111|November 11th, 2014]]<br />
* [[Developer_Meetings/20141103|November 3rd, 2014]]<br />
* [[Developer_Meetings/20141029|October 29th, 2014]]<br />
* [[Developer_Meetings/20141021|October 21st, 2014]]<br />
* [[Developer_Meetings/20141014|October 14th, 2014]]<br />
* [[Developer_Meetings/20141007|October 7th, 2014]]<br />
* [[Developer_Meetings/20140930|September 30th, 2014]]<br />
* [[Developer_Meetings/20140923|September 23rd, 2014]]<br />
* [[Developer_Meetings/20140916|September 16th, 2014]]<br />
* [[Developer_Meetings/20140909|September 9th, 2014]]<br />
* [[Developer_Meetings/20140901|September 1st, 2014]]<br />
* [[Developer_Meetings/20140826|August 26th, 2014]]<br />
* [[Developer_Meetings/20140819|August 19th, 2014]]<br />
* [[Developer_Meetings/20140812|August 12th, 2014]]<br />
* [[Developer_Meetings/20140805|August 5th, 2014]]<br />
* [[Developer_Meetings/20140729|July 29th, 2014]]<br />
* [[Developer_Meetings/20140722|July 22nd, 2014]]<br />
* [[Developer_Meetings/20140715-2|July 15th, 2014]] <small>Developer hangout</small><br />
* [[Developer_Meetings/20140715|July 15th, 2014]] <small>Extension Developers - From VTK5 to VTK6 - Q&A- Google Hangout</small><br />
* [[Developer_Meetings/20140701|July 1st, 2014]]<br />
* June 24th, 2014 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week 19th NA-MIC project week]</small><br />
* [[Developer_Meetings/20140617|June 17th, 2014]]<br />
* [[Developer_Meetings/20140610|June 10th, 2014]]<br />
* [[Developer_Meetings/20140603|June 3rd, 2014]]<br />
* [[Developer_Meetings/20140527|May 27th, 2014]]<br />
* [[Developer_Meetings/20140520|May 20th, 2014]]<br />
* [[Developer_Meetings/20140513|May 13th, 2014]]<br />
* May 6th, 2014 - <small>Cancelled - [http://www.commontk.org/index.php/CTK-Hackfest-May-2014 CTK Hackfest in St Louis]</small><br />
* [[Developer_Meetings/20140429|April 29th, 2014]]<br />
* [[Developer_Meetings/20140422|April 22th, 2014]]<br />
* [[Developer_Meetings/20140415|April 15th, 2014]]<br />
* [[Developer_Meetings/20140408|April 8th, 2014]]<br />
* [[Developer_Meetings/20140401|April 1st, 2014]]<br />
* [[Developer_Meetings/20140325|March 25th, 2014]]<br />
* [[Developer_Meetings/20140318|March 18th, 2014]]<br />
* [[Developer_Meetings/20140311|March 11th, 2014]]<br />
* [[Developer_Meetings/2014030607|March 6-7, 2014 (Face to Face in Boston)]]<br />
* [[Developer_Meetings/20140304|March 4th, 2014]]<br />
* [[Developer_Meetings/20140225|February 25th, 2014]]<br />
* [[Developer_Meetings/20140218|February 18th, 2014]]<br />
* [[Developer_Meetings/20140211|February 11th, 2014]]<br />
* [[Developer_Meetings/20140204|February 4th, 2014]]<br />
* [[Developer_Meetings/20140128|January 28th, 2014]]<br />
* [[Developer_Meetings/20140121|January 21st, 2014]]<br />
* [[Developer_Meetings/20140114|January 14th, 2014]]<br />
* January 7th, 2014 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/AHM_2014 AHM in Salt Lake City]</small><br />
<br />
== 2013 ==<br />
* December 31th, 2013 - <small>Cancelled - New year day</small><br />
* December 24th, 2013 - <small>Cancelled - Christmas day</small><br />
* [[Developer_Meetings/20131217|December 17, 2013]]<br />
* [[Developer_Meetings/20131210|December 10, 2013]]<br />
* [[Developer_Meetings/20131203|December 3rd, 2013]]<br />
* [[Developer_Meetings/20131126|November 26th, 2013]]<br />
* [[Developer_Meetings/20131119|November 19th, 2013]]<br />
* [[Developer_Meetings/20131112|November 12th, 2013]]<br />
* [[Developer_Meetings/20131105|November 5th, 2013]]<br />
* [[Developer_Meetings/20131029|October 29th, 2013]]<br />
* [[Developer_Meetings/20131022|October 22th, 2013]]<br />
* [[Developer_Meetings/20131015|October 15th, 2013]]<br />
* [[Developer_Meetings/20131008|October 8th, 2013]]<br />
* [[Developer_Meetings/20131001|October 1st, 2013]]<br />
* [[Developer_Meetings/20130924|September 24th, 2013]]<br />
* [[Developer_Meetings/20130917|September 17th, 2013]]<br />
* [[Developer_Meetings/20130910|September 10th, 2013]]<br />
* [[Developer_Meetings/20130903|September 3rd, 2013]]<br />
* [[Developer_Meetings/20130827|August 27th, 2013]]<br />
* [[Developer_Meetings/20130820|August 20th, 2013]]<br />
* [[Developer_Meetings/20130813|August 13th, 2013]]<br />
* [[Developer_Meetings/20130806|August 6th, 2013]]<br />
* [[Developer_Meetings/20130730|July 30th, 2013]]<br />
* [[Developer_Meetings/20130723|July 23rd, 2013]]<br />
* [[Developer_Meetings/20130716|July 16th, 2013]]<br />
* [[Developer_Meetings/20130709|July 9th, 2013]]<br />
* [[Developer_Meetings/20130702|July 2nd, 2013]]<br />
* June 18th, 23rd 2013 - cancelled due to NA-MIC Project week<br />
* [[Developer_Meetings/20130611|June 11th, 2013]]<br />
* [[Developer_Meetings/20130604|June 4th, 2013]]<br />
* [[Developer_Meetings/20130528|May 28th, 2013]]<br />
* May 21th, 2013 - <small>Cancelled - [http://www.commontk.org/index.php/CTK-Hackfest-May-2013 CTK Hackfest in Canada]</small><br />
* [[Developer_Meetings/20130514|May 14th, 2013]]<br />
* [[Developer_Meetings/20130507|May 7th, 2013]]<br />
* [[Developer_Meetings/20130430|April 30th, 2013]]<br />
* [[Developer_Meetings/20130423|April 23th, 2013]]<br />
* [[Developer_Meetings/20130416|April 16th, 2013]]<br />
* [[Developer_Meetings/20130409|April 9th, 2013]]<br />
* [[Developer_Meetings/20130402|April 2nd, 2013]]<br />
* [[Developer_Meetings/20130326|March 26th, 2013]]<br />
* [[Developer_Meetings/20130319|March 19th, 2013]]<br />
* [[Developer_Meetings/20130312|March 12th, 2013]]<br />
* [[Developer_Meetings/20130305|March 05th, 2013]]<br />
* [[Developer_Meetings/20130226|February 26th, 2013]]<br />
* [[Developer_Meetings/20130219|February 19th, 2013]]<br />
* [[Developer_Meetings/20130212|February 12th, 2013]]<br />
* [[Developer_Meetings/20130205|February 5th, 2013]]<br />
* [[Developer_Meetings/20130129|January 29th, 2013]]<br />
* [[Developer_Meetings/20130122|January 22nd, 2013]]<br />
* January 15th, 2013 - <small>Cancelled - AHM happened previous week</small><br />
* January 8th, 2013 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/AHM_2013 AHM in Salt Lake City]</small><br />
* January 1st, 2013 - <small>Cancelled - New year day</small><br />
<br />
== 2012 ==<br />
* December 25th, 2012 - <small>Cancelled - Christmas day</small><br />
* [[Developer_Meetings/20121218|December 18th, 2012]]<br />
* [[Developer_Meetings/20121211|December 11th, 2012]]<br />
* [[Developer_Meetings/20121204|December 4th, 2012]]<br />
* [[Developer_Meetings/20121127|November 27th, 2012]]<br />
* [[Developer_Meetings/20121120|November 20th, 2012]]<br />
* [[Developer_Meetings/20121113|November 13th, 2012]]<br />
* [[Developer_Meetings/20121106|November 6th, 2012]]<br />
* [[Developer_Meetings/20121030|October 30th, 2012]]<br />
* [[Developer_Meetings/20121023|October 23th, 2012]]<br />
* [[Developer_Meetings/20121016|October 16th, 2012]]<br />
* [[Developer_Meetings/20121009|October 09th, 2012]]<br />
* [[Developer_Meetings/20121002|October 02th, 2012]]<br />
* [[Developer_Meetings/20120925|September 25th, 2012]]<br />
* [[Developer_Meetings/20120918|September 18th, 2012]]<br />
* [[Developer_Meetings/20120911|September 11th, 2012]]<br />
* [[Developer_Meetings/20120904|September 4th, 2012]]<br />
* [[Developer_Meetings/20120828|August 28th, 2012]]<br />
* [[Developer_Meetings/20120821|August 21st, 2012]]<br />
* [[Developer_Meetings/20120814|August 14th, 2012]]<br />
* [[Developer_Meetings/20120807|August 7th, 2012]]<br />
* [[Developer_Meetings/20120731|July 31th, 2012]]<br />
* [[Developer_Meetings/20120724|July 24th, 2012]]<br />
* [[Developer_Meetings/20120717|July 17th, 2012]]<br />
* [[Developer_Meetings/20120710|July 10th, 2012]]<br />
* [[Developer_Meetings/20120703|July 3rd, 2012]]<br />
* [[Developer_Meetings/20120626|June 26th, 2012]]<br />
* [[Developer_Meetings/20120619|June 19th, 2012]]<br />
* [[Developer_Meetings/20120612|June 12th, 2012]]<br />
* [[Developer_Meetings/20120605|June 5th, 2012]]<br />
* [[Developer_Meetings/20120529|May 29, 2012]]<br />
* [[Developer_Meetings/20120522|May 22, 2012]]<br />
* [[Developer_Meetings/20120515|May 15, 2012]]<br />
* [[Developer_Meetings/20120508|May 8, 2012]]<br />
* [[Developer_Meetings/20120501|May 1st, 2012]]<br />
<br />
=== Miscellaneous ===<br />
* [http://wiki.na-mic.org/Wiki/index.php/Slicer4.2Planning August 20st, 2012 - Slicer 4.2 planning]<br />
<br />
== 2010 - 2011 ==<br />
* See [[Slicer4:QtPort/MeetingNotes]]<br />
<br />
== 2009 ==<br />
* September 16-17: [[Slicer:Developer_Meetings:20090916|Slicer widgets brainstorming]] (rough notes)<br />
* February 3: [[Slicer:Developer_Meetings:20090203|mBIRN preparation, Slicer3.4 release]]<br />
<br />
== 2008 ==<br />
* September 16: Demian on Python/Tractography<br />
* August 26: [[Slicer:Developer_Meetings:20080826|Slicer and NA-MIC Overview]]<br />
* August 11: [http://www.na-mic.org/Wiki/index.php/Slicer3_Q%26A_2008-11-18 Introduction of new researchers and developers (17 attendees)]<br />
* July 29: [[Slicer:Developer_Meetings:20080729|Slicer 3.2 release]]<br />
<br />
== 2007 ==<br />
* July 16: [[Slicer:Developer_Meetings:20070716|PNL demo Slicer3]]<br />
* June 12: [[Slicer:Developer_Meetings:20070612|PNL wishlist for Slicer3]]<br />
* March 27: [[Slicer:Developer_Meetings:20070327|Slicer 2.7, Slicer3 beta]]<br />
* February 6: [[Slicer:Developer_Meetings:20070206|Slicer3 mBIRN meeting Prep]]<br />
* January 30: [[Slicer:Developer_Meetings:20070130|Slicer3 Release Planning]]<br />
* January 2: [[Slicer:Developer_Meetings:20070102|Slicer3 AHM Prep]]<br />
<br />
== 2006 ==<br />
* November 21: [[Slicer:Developer_Meetings:20061121|Slicer3 Updates, preparations for retreat]]<br />
* November 07: [[Slicer:Developer_Meetings:20061107|Slicer3 Updates, NA-MIC Mesh Kickoff]]<br />
* October 10: [[Slicer:Developer_Meetings:20061010| Slicer3 Updates]]<br />
* August 29: [[Slicer:Developer_Meetings:20060829|Slicer 3 and Slicer 2.6 bugs]]<br />
* May 2: [[Slicer:Developer_Meetings:20060502|Release 2.6, Fiducials, Slicer for MRT]]<br />
* March 14: [[Slicer:Developer_Meetings:20060314|Release 2.6, mBIRN meeting, Slicer MRT]]<br />
<br />
<br />
== 2005 ==<br />
* June 7: [[Slicer:Developer_Meetings:20050607|NA-MIC Programming Week discussion: Slicer 3]]<br />
* May 24: [[Slicer:Developer_Meetings:20050524|Release 2.5]]<br />
* May 10: [[Slicer:Developer_Meetings:20050510|Release 2.5]]<br />
* April 11: [[Slicer:Developer_Meetings:20050411|To-do list for release 2.5, OpenTracker]]<br />
* March 29: [[Slicer:Developer_Meetings:20050329|Dan Kacher : Integrating trackers with Slicer ]]<br />
* March 15: [[Slicer:Developer_Meetings:20050315|Updates from BIRN Meeting, Training, Windows Building, Release 2.5]]<br />
* March 1: [[Slicer:Developer_Meetings:20050301|Updates from NA-MIC Meeting, Current and Future Projects]]<br />
* February 1: [[Slicer:Developer_Meetings:20050201|Randy Ellis : demo of surgical navigation system]]<br />
* January 18: [[Slicer:Developer_Meetings:20050118|Slicer Architecture]]</div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Labs/OpenCV&diff=44645Documentation/Labs/OpenCV2016-01-14T20:32:17Z<p>Nicole: /* Status */</p>
<hr />
<div>=Background=<br />
<br />
OpenCV is required for image processing tasks of a funded project that intends to use 3D Slicer for automating annotation of digital pathology images. It is also required by several other projects that plan to use OpenCV.<br />
<br />
=Approach=<br />
<br />
Build an extension SlicerOpenCV that encapsulates OpenCV libraries, and provides configuration/testing modules for the developers, but no end-user functionality. Implement user-level functionality in separate extensions that would depend on SlicerOpenCV.<br />
<br />
Extensions that need OpenCV would declare SlicerOpenCV as a dependency, which would automatically fetch the extension on install from the Extension Manager, or initialize all necessary paths to the libraries for building a dependent module. This extension will also build ITK OpenCVBridge module to facilitate integration with ITK-based applications.<br />
<br />
We should also consider building pydicom as part of that extension.<br />
<br />
=Alternative approaches considered=<br />
<br />
Other options discussed were:<br />
<br />
* installation of OpenCV from binary package (discarded due to incompatibility of the compilers used for OpenCV and Slicer packaged builds on Windows)<br />
* reuse of the Anaconda (discarded due to the present lack of integration of anaconda (in progress), and the fact that pyopencv is not a standard package)<br />
* superbuild of OpenCV within an extension providing user-level functionality (discarded since this would not allow the reuse of OpenCV libraries across extensions, and we see several potential users)<br />
<br />
=Unresolved questions=<br />
<br />
* what OpenCV packages are needed by the target users?<br />
* are Intel-specific of GPU-specific computational libraries needed? (these have licensing restrictions)<br />
<br />
Answers:<br />
* SBU (Yi): Matrices, color space conversion, iso contour extraction<br />
** source code at [https://github.com/SBU-BMI/u24-software/tree/master/analysis-library/yi-codes/src SBU-BMI (private)] includes opencv.hpp and gpu.hpp<br />
* Montreal group (MNI, Louis Collins): only need camera calibration and basic functionality to track colored objects in video; no GPU or Intel libraries needed<br />
<br />
=Status=<br />
<br />
* Jan 2016:<br />
** Slicer's version of ITK has been patched to allow building the OpenCV bridge module externally, SlicerOpenCV updated to use that functionality.<br />
** Work is in progress to provide CMake configuration files to easily allow other extensions to build against SlicerOpenCV<br />
* Dec 2015: Initial tree of the extension is available publicly https://github.com/SBU-BMI/SlicerOpenCV<br />
* Oct 2015: Initial discussions and initial plan completed. Update posted to the developer list [1].<br />
<br />
=References=<br />
[1] http://slicer-devel.65872.n3.nabble.com/OpenCV-in-Slicer-td4035068.html</div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/4.5/Modules/Markups&diff=44569Documentation/4.5/Modules/Markups2016-01-06T18:20:54Z<p>Nicole: /* File Format */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Author: Nicole Aucoin, SPL, BWH<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module is used to manage markups in Slicer. <br />
<br />
It is based on the functionality in the Slicer 3.6 Fiducials module, with elements from the Slicer 4.2 Annotations module. <br />
<br />
Currently, only fiducials are supported.<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
<br />
Development history can be found in the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
This module allows you to add new markups, edit markups in a list, delete markups and modify display properties of markups.<br />
<br />
Markups can be passed to command line modules (CLIs) using the <pre>--point</pre> or <pre>--pointfile</pre> argument. <br />
<br />
The Mouse mode tool bar can be used to place new markups by positioning the mouse and left clicking in the viewers. Once you are in Place mode and placing Markups fiducials, you can use the 'p' key to place a new fiducial while the Markups GUI is open. You can also use a right button click to stop placing fiducials when in persistent mode.<br />
<br />
You can place fiducials and use the GUI to jump slices or the 3D view to those locations. If you select fiducials in the table, you can right click to get the summed linear distance between their locations.<br />
<br />
The Markups module can convert Annotation fiducials into Markups fiducials, and will offer the user the option of doing it automatically when the Markups GUI is entered. There is also a manual button under the Advanced tab.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
<br />
== Panels ==<br />
<br />
<gallery><br />
File:Markups-GUI-Collapsed.png | GUI<br />
File:Markups-ModifyList.png | Select the active list, set visibility and lock flags, set uniform scale.<br />
File:Markups-JumpSlices-44.png | Jump the 2D slice view windows to the coordinates of the highlighted markup.<br />
File:Markups-ModifyMarkupsInList.png | Modify Markups in list: toggle visibility, selected, and lock flags, delete.<br />
File:Markups-Table.png | Table showing the fiducials in the active Markups list<br />
File:Markups-Advanced.png | Advanced panel: move markups up or down, add a markup, name format, convert annotation fiducials, display properties for the list of markups<br />
File:Markups-DisplayProperties.png | Display properties, inside the Advaned panel, includes 2d projection settings.<br />
File:Markups-MouseToolbar.png | Place Markup fiducials by setting the Mouse mode in the tool bar<br />
</gallery><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
*[[Documentation/Nightly/Modules/Annotations | Annotations]] module is similar, and will be deprecated as the functionality is moved to the Markups module.<br />
*[https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Endoscopy/Endoscopy.py#L303 Endoscopy module] uses fiducials<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
*[http://wiki.na-mic.org/Wiki/index.php/2013_Summer_Project_Week:MarkupsModuleSummer2013 Summer 2013 Project Week project page]<br />
*[http://wiki.na-mic.org/Wiki/index.php/2013_Project_Week:MarkupsModule Winter 2013 Project Week project page]<br />
*[http://wiki.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:AnnotationModule Summer 2012 Project Week project page]<br />
<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
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<br />
== Python ==<br />
<br />
=== Open the Markups Module ===<br />
<br />
You can set the Markups module gui to be the current module gui using this command:<br />
<br />
slicer.util.mainWindow().moduleSelector().selectModule('Markups')<br />
<br />
=== Load From File ===<br />
<br />
Markups fiducials can be loaded from file:<br />
<br />
slicer.util.loadMarkupsFiducialList('/path/to/list/F.fcsv')<br />
<br />
=== Adding Fiducials Programatically ===<br />
<br />
Markups fiducials can be added to the currently active list from the python console by using the following module logic command:<br />
<br />
slicer.modules.markups.logic().AddFiducial()<br />
<br />
The command with no arguments will place a new fiducial at the origin. You can also pass it an initial location:<br />
<br />
slicer.modules.markups.logic().AddFiducial(1.0, -2.0, 3.3)<br />
<br />
=== Adding Fiducials via Mouse Clicks ===<br />
<br />
You can also set the mouse mode into Markups fiducial placement by calling:<br />
<br />
placeModePersistence = 1<br />
slicer.modules.markups.logic().StartPlaceMode(placeModePersistence)<br />
<br />
A lower level way to do this is via the selection and interaction nodes:<br />
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")<br />
selectionNode.SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode")<br />
interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")<br />
placeModePersistence = 1<br />
interactionNode.SetPlaceModePersistence(placeModePersistence)<br />
# mode 1 is Place, can also be accessed via slicer.vtkMRMLInteractionNode().Place<br />
interactionNode.SetCurrentInteractionMode(1)<br />
<br />
To switch back to view transform once you're done placing fiducials:<br />
interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")<br />
interactionNode.SwitchToViewTransformMode()<br />
# also turn off place mode persistence if required<br />
interactionNode.SetPlaceModePersistence(0)<br />
<br />
=== Access to Fiducial Properties ===<br />
<br />
Each vtkMRMLMarkupsFiducialNode has a vector of points in it which can be accessed from python:<br />
<br />
fidNode = getNode("vtkMRMLMarkupsFiducialNode1")<br />
n = fidNode.AddFiducial(4.0, 5.5, -6.0)<br />
fidNode.SetNthFiducialLabel(n, "new label")<br />
# each markup is given a unique id which can be accessed from the superclass level<br />
id1 = fidNode.GetNthMarkupID(n)<br />
# manually set the position<br />
fidNode.SetNthFiducialPosition(n, 6.0, 7.0, 8.0)<br />
# set the label<br />
fidNode.SetNthFiducialLabel(n, "New label")<br />
# set the selected flag, only selected = 1 fiducials will be passed to CLIs<br />
fidNode.SetNthFiducialSelected(n, 1)<br />
# set the visibility flag<br />
fidNode.SetNthFiducialVisibility(n, 0) <br />
<br />
You can loop over the fiducials in a list and get the coordinates:<br />
<br />
fidList = slicer.util.getNode('F')<br />
numFids = fidList.GetNumberOfFiducials()<br />
for i in range(numFids):<br />
ras = [0,0,0]<br />
fidList.GetNthFiducialPosition(i,ras)<br />
# the world position is the RAS position with any transform matrices applied<br />
world = [0,0,0,0]<br />
fidList.GetNthFiducialWorldCoordinates(0,world)<br />
print i,": RAS =",ras,", world =",world<br />
<br />
You can also look at the sample code in the [https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Endoscopy/Endoscopy.py#L287 Endoscopy module] to see how python is used to access fiducials from a scripted module.<br />
<br />
=== VTK Widget access ===<br />
<br />
The Markups 3D fiducial displayable manager can be accessed from python allowing debugging of the vtkSeedWidget:<br />
<br />
fidNode = slicer.mrmlScene.GetNodeByID("vtkMRMLMarkupsFiducialNode1")<br />
lm = slicer.app.layoutManager()<br />
td = lm.threeDWidget(0)<br />
ms = vtk.vtkCollection()<br />
td.getDisplayableManagers(ms)<br />
for i in range(ms.GetNumberOfItems()): <br />
m = ms.GetItemAsObject(i)<br />
if m.GetClassName() == "vtkMRMLMarkupsFiducialDisplayableManager3D":<br />
print i, m.GetClassName()<br />
h = m.GetHelper()<br />
seedWidget = h.GetWidget(fidNode)<br />
seedRepresentation = seedWidget.GetSeedRepresentation()<br />
handleRep2 = seedRepresentation.GetHandleRepresentation(2)<br />
print handleRep2.GetDisplayPosition()<br />
print handleRep2.GetWorldPosition()<br />
<br />
<br />
The Markups 2D fiducial displayable manager can be accessed from python as well to debug the seed widget in 2D. For the Red slice viewer:<br />
<br />
fidNode = slicer.mrmlScene.GetNodeByID("vtkMRMLMarkupsFiducialNode1")<br />
lm = slicer.app.layoutManager()<br />
redWidget = lm.sliceWidget("Red")<br />
redView = redWidget.sliceView()<br />
ms = vtk.vtkCollection()<br />
redView.getDisplayableManagers(ms)<br />
for i in range(ms.GetNumberOfItems()):<br />
m = ms.GetItemAsObject(i)<br />
if m.GetClassName() == "vtkMRMLMarkupsFiducialDisplayableManager2D":<br />
print i, m.GetClassName()<br />
h = m.GetHelper()<br />
seedWidget = h.GetWidget(fidNode)<br />
seedRepresentation = seedWidget.GetSeedRepresentation()<br />
handleRep = seedRepresentation.GetHandleRepresentation(0)<br />
print handleRep.GetDisplayPosition()<br />
<br />
== C++ ==<br />
<br />
===Selection and Interaction===<br />
<br />
For the selection and interaction nodes, make sure that you access the singleton nodes already in the scene (rather than making your own) via (caveat: this call works on displayable managers, you may have to go a different route to get at the application logic):<br />
vtkMRMLApplicationLogic *mrmlAppLogic = this->GetMRMLApplicationLogic();<br />
vtkMRMLInteractionNode *inode = mrmlAppLogic->GetInteractionNode();<br />
vtkMRMLSelectionNode *snode = mrmlAppLogic->GetSelectionNode();<br />
If you can't get at the mrml application logic, you can get the nodes from the scene:<br />
vtkMRMLInteractionNode *interactionNode = vtkMRMLInteractionNode::SafeDownCast(this->GetMRMLScene()->GetNodeByID("vtkMRMLInteractionNodeSingleton"));<br />
<br />
You can then call methods on the nodes or add your own event observers as in<br />
vtkSlicerMarkupsModuleLogic::ObserveMRMLScene<br />
You can see vtkSlicerMarkupsModuleLogic::ProcessMRMLNodesEvents to see how to respond to interaction node changes.<br />
<br />
Slicer4/Base/QTGUI/qSlicerMouseModeToolBar.cxx has a lot of the code you'll need as well, with a slightly different way of getting at the mrml app logic to access the nodes.<br />
<br />
The calls you need to make to switch into placing fiducials with the mouse are:<br />
selectionNode->SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode");<br />
interactionNode->SetCurrentInteractionMode(vtkMRMLInteractionNode::Place);<br />
If you don't set PlaceModePersistence on the interaction node to 1, the mouse mode/current interaction mode will automatically go back to view transform after one fiducial has been placed, and you just need to reset the current interaction mode for future placing (the active place node class name and ID are persistent).<br />
<br />
=== Programmatic Access to Fiducials ===<br />
<br />
This section explains how to access fiducial nodes added into the scene by the user.<br />
<br />
In your module's Logic class, overwrite SetMRMLSceneInternal to observe the NodeAddedEvent of the scene:<br />
void vtkSlicerMYMODULEModuleLogic::SetMRMLSceneInternal(vtkMRMLScene * newScene)<br />
{<br />
vtkNew<vtkIntArray> events;<br />
events->InsertNextValue(vtkMRMLScene::NodeAddedEvent);<br />
// Optionally you can add more events here, <br />
// such as vtkMRMLScene::NodeRemovedEvent<br />
this->SetAndObserveMRMLSceneEventsInternal(newScene, events.GetPointer());<br />
}<br />
Via the set and observe mrml scene macro, anytime a node is added into the scene, it will trigger the base Logic class method<br />
[http://slicer.org/doc/html/classvtkMRMLAbstractLogic.html#a51fdf00ecfc18c1a1465d4bccb789ef1 vtkMRMLAbstractLogic::ProcessMRMLNodesEvents] which calls the virtual method <code>vtkMRMLAbstractLogic::OnMRMLSceneNodeAdded(vtkMRMLNode* node)</code><br />
Reimplement that method in your logic class:<br />
void vtkSlicerMYMODULEModuleLogic::OnMRMLSceneNodeAdded(vtkMRMLNode* addedNode)<br />
{<br />
vtkMRMLMarkupsFiducialNode* fidNode =<br />
vtkMRMLMarkupsFiducialNode::SafeDownCast(addedNode);<br />
if (fidNode)<br />
{<br />
// here you write what you need to do when a <br />
// fiducial node is added into the scene<br />
}<br />
}<br />
<br />
=== File Format===<br />
<br />
The Markups Fiducial storage node uses a comma separated value file to store the fiducials on disk. The format is:<br />
<br />
A leading comment line giving the Slicer version number:<br />
# Markups fiducial file version = 4.5<br />
A comment line giving the coordinate system, RAS = 0, LPS = 1, IJK = 2 (IJK is currently not supported, RAS is printed instead)<br />
# CoordinateSystem = 0<br />
A comment line explaining the fields in the csv<br />
# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID<br />
Then comes the fiducials, one per line, for example:<br />
vtkMRMLMarkupsFiducialNode_0,1.29,-40.18,60.15,0,0,0,1,1,1,0,F-1,,<br />
*id = a string giving a unique id for this fiducial, usually based on the class name<br />
*x,y,z = the floating point coordinate of the fiducial point<br />
*ow,ox,oy,oz = the orientation quaternion of this fiducial, angle and axis, default 0,0,0,1 (or 0,0,0,0,0,0,1.0)<br />
*vis = the visibility flag for this fiducial, 0 or 1, default 1<br />
*sel = the selected flag for this fiducial, 0 or 1, default 1<br />
*lock = the locked flag for this fiducial, 0 or 1, default 0<br />
*label = the name for this fiducial, displayed beside the glyph, with quotes around it if there is a comma in the field<br />
*desc = a string description for this fiducial, optional<br />
*associatedNodeID = an id of a node in the scene with which the fiducial is associated, for example the volume or model on which the fiducial was placed, optional<br />
<br />
The file can be parsed using stringstream and getline:<br />
<br />
std::fstream fstr;<br />
fstr.open(fileName.c_str(), std::fstream::in);<br />
char line[1024];<br />
while (fstr.good())<br />
{<br />
fstr.getline(line, 1024);<br />
std::stringstream ss(line);<br />
std::string component;<br />
getline(ss, component, ',');<br />
[...]<br />
}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/Markups&diff=44568Documentation/Nightly/Modules/Markups2016-01-06T18:19:11Z<p>Nicole: /* File Format */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Author: Nicole Aucoin, SPL, BWH<br><br />
Contact: Nicole Aucoin, <email>nicole@bwh.harvard.edu</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
This module is used to manage markups in Slicer. <br />
<br />
It is based on the functionality in the Slicer 3.6 Fiducials module, with elements from the Slicer 4.2 Annotations module. <br />
<br />
Currently, only fiducials are supported.<br />
<br />
{{documentation/{{documentation/version}}/module-description}}<br />
<br />
Development history can be found in the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]].<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
This module allows you to add new markups, edit markups in a list, delete markups and modify display properties of markups.<br />
<br />
Markups can be passed to command line modules (CLIs) using the <pre>--point</pre> or <pre>--pointfile</pre> argument. <br />
<br />
The Mouse mode tool bar can be used to place new markups by positioning the mouse and left clicking in the viewers. Once you are in Place mode and placing Markups fiducials, you can use the 'p' key to place a new fiducial while the Markups GUI is open. You can also use a right button click to stop placing fiducials when in persistent mode.<br />
<br />
You can place fiducials and use the GUI to jump slices or the 3D view to those locations. If you select fiducials in the table, you can right click to get the summed linear distance between their locations.<br />
<br />
The Markups module can convert Annotation fiducials into Markups fiducials, and will offer the user the option of doing it automatically when the Markups GUI is entered. There is also a manual button under the Advanced tab.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
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N/A<br />
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<br />
== Panels ==<br />
<br />
<gallery><br />
File:Markups-GUI-Collapsed.png | GUI<br />
File:Markups-ModifyList.png | Select the active list, set visibility and lock flags, set uniform scale.<br />
File:Markups-JumpSlices-44.png | Jump the 2D slice view windows to the coordinates of the highlighted markup.<br />
File:Markups-ModifyMarkupsInList.png | Modify Markups in list: toggle visibility, selected, and lock flags, delete.<br />
File:Markups-Table.png | Table showing the fiducials in the active Markups list<br />
File:Markups-Advanced.png | Advanced panel: move markups up or down, add a markup, name format, convert annotation fiducials, display properties for the list of markups<br />
File:Markups-DisplayProperties.png | Display properties, inside the Advaned panel, includes 2d projection settings.<br />
File:Markups-MouseToolbar.png | Place Markup fiducials by setting the Mouse mode in the tool bar<br />
</gallery><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
<br />
*[[Documentation/Nightly/Modules/Annotations | Annotations]] module is similar, and will be deprecated as the functionality is moved to the Markups module.<br />
*[https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Endoscopy/Endoscopy.py#L303 Endoscopy module] uses fiducials<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
<br />
*[http://wiki.na-mic.org/Wiki/index.php/2013_Summer_Project_Week:MarkupsModuleSummer2013 Summer 2013 Project Week project page]<br />
*[http://wiki.na-mic.org/Wiki/index.php/2013_Project_Week:MarkupsModule Winter 2013 Project Week project page]<br />
*[http://wiki.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:AnnotationModule Summer 2012 Project Week project page]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo}}<br />
<br />
== Python ==<br />
<br />
=== Open the Markups Module ===<br />
<br />
You can set the Markups module gui to be the current module gui using this command:<br />
<br />
slicer.util.mainWindow().moduleSelector().selectModule('Markups')<br />
<br />
=== Load From File ===<br />
<br />
Markups fiducials can be loaded from file:<br />
<br />
slicer.util.loadMarkupsFiducialList('/path/to/list/F.fcsv')<br />
<br />
=== Adding Fiducials Programatically ===<br />
<br />
Markups fiducials can be added to the currently active list from the python console by using the following module logic command:<br />
<br />
slicer.modules.markups.logic().AddFiducial()<br />
<br />
The command with no arguments will place a new fiducial at the origin. You can also pass it an initial location:<br />
<br />
slicer.modules.markups.logic().AddFiducial(1.0, -2.0, 3.3)<br />
<br />
=== Adding Fiducials via Mouse Clicks ===<br />
<br />
You can also set the mouse mode into Markups fiducial placement by calling:<br />
<br />
placeModePersistence = 1<br />
slicer.modules.markups.logic().StartPlaceMode(placeModePersistence)<br />
<br />
A lower level way to do this is via the selection and interaction nodes:<br />
selectionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLSelectionNodeSingleton")<br />
selectionNode.SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode")<br />
interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")<br />
placeModePersistence = 1<br />
interactionNode.SetPlaceModePersistence(placeModePersistence)<br />
# mode 1 is Place, can also be accessed via slicer.vtkMRMLInteractionNode().Place<br />
interactionNode.SetCurrentInteractionMode(1)<br />
<br />
To switch back to view transform once you're done placing fiducials:<br />
interactionNode = slicer.mrmlScene.GetNodeByID("vtkMRMLInteractionNodeSingleton")<br />
interactionNode.SwitchToViewTransformMode()<br />
# also turn off place mode persistence if required<br />
interactionNode.SetPlaceModePersistence(0)<br />
<br />
=== Access to Fiducial Properties ===<br />
<br />
Each vtkMRMLMarkupsFiducialNode has a vector of points in it which can be accessed from python:<br />
<br />
fidNode = getNode("vtkMRMLMarkupsFiducialNode1")<br />
n = fidNode.AddFiducial(4.0, 5.5, -6.0)<br />
fidNode.SetNthFiducialLabel(n, "new label")<br />
# each markup is given a unique id which can be accessed from the superclass level<br />
id1 = fidNode.GetNthMarkupID(n)<br />
# manually set the position<br />
fidNode.SetNthFiducialPosition(n, 6.0, 7.0, 8.0)<br />
# set the label<br />
fidNode.SetNthFiducialLabel(n, "New label")<br />
# set the selected flag, only selected = 1 fiducials will be passed to CLIs<br />
fidNode.SetNthFiducialSelected(n, 1)<br />
# set the visibility flag<br />
fidNode.SetNthFiducialVisibility(n, 0) <br />
<br />
You can loop over the fiducials in a list and get the coordinates:<br />
<br />
fidList = slicer.util.getNode('F')<br />
numFids = fidList.GetNumberOfFiducials()<br />
for i in range(numFids):<br />
ras = [0,0,0]<br />
fidList.GetNthFiducialPosition(i,ras)<br />
# the world position is the RAS position with any transform matrices applied<br />
world = [0,0,0,0]<br />
fidList.GetNthFiducialWorldCoordinates(0,world)<br />
print i,": RAS =",ras,", world =",world<br />
<br />
You can also look at the sample code in the [https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/Endoscopy/Endoscopy.py#L287 Endoscopy module] to see how python is used to access fiducials from a scripted module.<br />
<br />
=== VTK Widget access ===<br />
<br />
The Markups 3D fiducial displayable manager can be accessed from python allowing debugging of the vtkSeedWidget:<br />
<br />
fidNode = slicer.mrmlScene.GetNodeByID("vtkMRMLMarkupsFiducialNode1")<br />
lm = slicer.app.layoutManager()<br />
td = lm.threeDWidget(0)<br />
ms = vtk.vtkCollection()<br />
td.getDisplayableManagers(ms)<br />
for i in range(ms.GetNumberOfItems()): <br />
m = ms.GetItemAsObject(i)<br />
if m.GetClassName() == "vtkMRMLMarkupsFiducialDisplayableManager3D":<br />
print i, m.GetClassName()<br />
h = m.GetHelper()<br />
seedWidget = h.GetWidget(fidNode)<br />
seedRepresentation = seedWidget.GetSeedRepresentation()<br />
handleRep2 = seedRepresentation.GetHandleRepresentation(2)<br />
print handleRep2.GetDisplayPosition()<br />
print handleRep2.GetWorldPosition()<br />
<br />
<br />
The Markups 2D fiducial displayable manager can be accessed from python as well to debug the seed widget in 2D. For the Red slice viewer:<br />
<br />
fidNode = slicer.mrmlScene.GetNodeByID("vtkMRMLMarkupsFiducialNode1")<br />
lm = slicer.app.layoutManager()<br />
redWidget = lm.sliceWidget("Red")<br />
redView = redWidget.sliceView()<br />
ms = vtk.vtkCollection()<br />
redView.getDisplayableManagers(ms)<br />
for i in range(ms.GetNumberOfItems()):<br />
m = ms.GetItemAsObject(i)<br />
if m.GetClassName() == "vtkMRMLMarkupsFiducialDisplayableManager2D":<br />
print i, m.GetClassName()<br />
h = m.GetHelper()<br />
seedWidget = h.GetWidget(fidNode)<br />
seedRepresentation = seedWidget.GetSeedRepresentation()<br />
handleRep = seedRepresentation.GetHandleRepresentation(0)<br />
print handleRep.GetDisplayPosition()<br />
<br />
== C++ ==<br />
<br />
===Selection and Interaction===<br />
<br />
For the selection and interaction nodes, make sure that you access the singleton nodes already in the scene (rather than making your own) via (caveat: this call works on displayable managers, you may have to go a different route to get at the application logic):<br />
vtkMRMLApplicationLogic *mrmlAppLogic = this->GetMRMLApplicationLogic();<br />
vtkMRMLInteractionNode *inode = mrmlAppLogic->GetInteractionNode();<br />
vtkMRMLSelectionNode *snode = mrmlAppLogic->GetSelectionNode();<br />
If you can't get at the mrml application logic, you can get the nodes from the scene:<br />
vtkMRMLInteractionNode *interactionNode = vtkMRMLInteractionNode::SafeDownCast(this->GetMRMLScene()->GetNodeByID("vtkMRMLInteractionNodeSingleton"));<br />
<br />
You can then call methods on the nodes or add your own event observers as in<br />
vtkSlicerMarkupsModuleLogic::ObserveMRMLScene<br />
You can see vtkSlicerMarkupsModuleLogic::ProcessMRMLNodesEvents to see how to respond to interaction node changes.<br />
<br />
Slicer4/Base/QTGUI/qSlicerMouseModeToolBar.cxx has a lot of the code you'll need as well, with a slightly different way of getting at the mrml app logic to access the nodes.<br />
<br />
The calls you need to make to switch into placing fiducials with the mouse are:<br />
selectionNode->SetReferenceActivePlaceNodeClassName("vtkMRMLMarkupsFiducialNode");<br />
interactionNode->SetCurrentInteractionMode(vtkMRMLInteractionNode::Place);<br />
If you don't set PlaceModePersistence on the interaction node to 1, the mouse mode/current interaction mode will automatically go back to view transform after one fiducial has been placed, and you just need to reset the current interaction mode for future placing (the active place node class name and ID are persistent).<br />
<br />
=== Programmatic Access to Fiducials ===<br />
<br />
This section explains how to access fiducial nodes added into the scene by the user.<br />
<br />
In your module's Logic class, overwrite SetMRMLSceneInternal to observe the NodeAddedEvent of the scene:<br />
void vtkSlicerMYMODULEModuleLogic::SetMRMLSceneInternal(vtkMRMLScene * newScene)<br />
{<br />
vtkNew<vtkIntArray> events;<br />
events->InsertNextValue(vtkMRMLScene::NodeAddedEvent);<br />
// Optionally you can add more events here, <br />
// such as vtkMRMLScene::NodeRemovedEvent<br />
this->SetAndObserveMRMLSceneEventsInternal(newScene, events.GetPointer());<br />
}<br />
Via the set and observe mrml scene macro, anytime a node is added into the scene, it will trigger the base Logic class method<br />
[http://slicer.org/doc/html/classvtkMRMLAbstractLogic.html#a51fdf00ecfc18c1a1465d4bccb789ef1 vtkMRMLAbstractLogic::ProcessMRMLNodesEvents] which calls the virtual method <code>vtkMRMLAbstractLogic::OnMRMLSceneNodeAdded(vtkMRMLNode* node)</code><br />
Reimplement that method in your logic class:<br />
void vtkSlicerMYMODULEModuleLogic::OnMRMLSceneNodeAdded(vtkMRMLNode* addedNode)<br />
{<br />
vtkMRMLMarkupsFiducialNode* fidNode =<br />
vtkMRMLMarkupsFiducialNode::SafeDownCast(addedNode);<br />
if (fidNode)<br />
{<br />
// here you write what you need to do when a <br />
// fiducial node is added into the scene<br />
}<br />
}<br />
<br />
=== File Format===<br />
<br />
The Markups Fiducial storage node uses a comma separated value file to store the fiducials on disk. The format is:<br />
<br />
A leading comment line giving the Slicer version number:<br />
# Markups fiducial file version = 4.5<br />
A comment line giving the coordinate system, RAS = 0, LPS = 1, IJK = 2 (IJK is currently not supported, RAS is printed instead)<br />
# CoordinateSystem = 0<br />
A comment line explaining the fields in the csv<br />
# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID<br />
Then comes the fiducials, one per line, for example:<br />
vtkMRMLMarkupsFiducialNode_0,1.29,-40.18,60.15,0,0,0,1,1,1,0,F-1,,<br />
*id = a string giving a unique id for this fiducial, usually based on the class name<br />
*x,y,z = the floating point coordinate of the fiducial point<br />
*ow,ox,oy,oz = the orientation quaternion of this fiducial, angle and axis, default 0,0,0,1 (or 0,0,0,0,0,0,1.0)<br />
*vis = the visibility flag for this fiducial, 0 or 1, default 1<br />
*sel = the selected flag for this fiducial, 0 or 1, default 1<br />
*lock = the locked flag for this fiducial, 0 or 1, default 0<br />
*label = the name for this fiducial, displayed beside the glyph, with quotes around it if there is a comma in the field<br />
*desc = a string description for this fiducial, optional<br />
*associatedNodeID = an id of a node in the scene with which the fiducial is associated, for example the volume or model on which the fiducial was placed, optional<br />
<br />
The file can be parsed using stringstream and getline:<br />
<br />
std::fstream fstr;<br />
fstr.open(fileName.c_str(), std::fstream::in);<br />
char line[1024];<br />
while (fstr.good())<br />
{<br />
fstr.getline(line, 1024);<br />
std::stringstream ss(line);<br />
std::string component;<br />
getline(ss, component, ',');<br />
[...]<br />
}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Labs/OpenCV&diff=43263Documentation/Labs/OpenCV2015-11-05T19:52:15Z<p>Nicole: /* Unresolved questions */</p>
<hr />
<div>=Background=<br />
<br />
OpenCV is required for image processing tasks of a funded project that intends to use 3D Slicer for automating annotation of digital pathology images. It is also required by several other projects that plan to use OpenCV.<br />
<br />
=Approach=<br />
<br />
Build an extension SlicerOpenCV that encapsulates OpenCV libraries, and provides configuration/testing modules for the developers, but no end-user functionality. Implement user-level functionality in separate extensions that would depend on SlicerOpenCV.<br />
<br />
Extensions that need OpenCV would declare SlicerOpenCV as a dependency, which would automatically fetch the extension on install from the Extension Manager, or initialize all necessary paths to the libraries for building a dependent module. This extension will also build ITK OpenCVBridge module to facilitate integration with ITK-based applications.<br />
<br />
We should also consider building pydicom as part of that extension.<br />
<br />
=Alternative approaches considered=<br />
<br />
Other options discussed were:<br />
<br />
* installation of OpenCV from binary package (discarded due to incompatibility of the compilers used for OpenCV and Slicer packaged builds on Windows)<br />
* reuse of the Anaconda (discarded due to the present lack of integration of anaconda (in progress), and the fact that pyopencv is not a standard package)<br />
* superbuild of OpenCV within an extension providing user-level functionality (discarded since this would not allow the reuse of OpenCV libraries across extensions, and we see several potential users)<br />
<br />
=Unresolved questions=<br />
<br />
* what OpenCV packages are needed by the target users?<br />
* are Intel-specific of GPU-specific computational libraries needed? (these have licensing restrictions)<br />
<br />
Answers:<br />
* SBU (Yi): Matrices, color space conversion, iso contour extraction<br />
** source code at [https://github.com/SBU-BMI/u24-software/tree/master/analysis-library/yi-codes/src SBU-BMI (private)] includes opencv.hpp and gpu.hpp<br />
* Montreal group (MNI, Louis Collins): only need camera calibration and basic functionality to track colored objects in video; no GPU or Intel libraries needed<br />
<br />
=Status=<br />
<br />
Initial discussions and initial plan completed. Update posted to the developer list [1].<br />
<br />
=References=<br />
[1] http://slicer-devel.65872.n3.nabble.com/OpenCV-in-Slicer-td4035068.html</div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Announcements&diff=43202Documentation/Nightly/Announcements2015-11-02T16:08:30Z<p>Nicole: /* Markups */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
__NOTOC__<br />
<br />
<br />
<br />
{|width="100%"<br />
|align="center"|<br />
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]<br />
|}<br />
<br />
<br />
{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"<br />
|[[#Summary|Summary ]]<br />
|[[#What is 3D Slicer|What is 3D Slicer]]<br />
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]<br />
|[[#Slicer Training|Slicer Training]]<br />
|[[#Slicer Extensions|Slicer Extensions]]<br />
|[[#Other Improvements, Additions & Documentation|Other Improvements, Additions & Documentation]]<br />
|}<br />
<br />
= Summary = <br />
<br />
The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.<br />
<br />
* Slicer {{documentation/version}} introduces <br />
** An improved App Store, known as the Extension Manager, for adding plug-ins to Slicer. More than 80 plug-ins and packages of plug-ins are currently available.<br />
** Close to 150 feature improvements and bug fixes have resulted in improved performance and stability.<br />
** Improvements to many modules.<br />
<br />
* Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and the bug tracker. <br />
* Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.<br />
* The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of tutorials and data sets for training in the use of Slicer. <br />
<br />
[http://www.slicer.org slicer.org] is the portal to the application, training materials, and the development community.<br />
<br />
= What is 3D Slicer =<br />
{{:Documentation/{{documentation/version}}/Slicer}}<br />
<br />
= Slicer {{documentation/version}} Highlights =<br />
<br />
<gallery caption="New and Improved Modules" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:Grid3dVolume.png|Improved [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module with support for non-linear transforms, visualization of transforms in 2D and 3D, detailed transform properties view - '''[https://www.youtube.com/watch?v=kZUAfR0mqqI click here for demo video]'''.<ul><li>Added support for copy/paste of linear transforms</li><li>Support saving of any transform to a grid transform</li><li> Improved composite transform support</li><li>Added support for thin plate spline transforms</li><li>Addressed display issue for slice intersection display of non-linearly transformed model</li></ul><br />
<br />
Image:DICOM Screenshot.png |The user interface of the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module has been improved for a better usability.<ul><li>Improved DICOM browser adding a right click menu to allow deleting or exporting to disk at the patients/studies/series levels.</li><li>Added support for DICOM private dictionary.</li><li>Improved support for loading of DICOM referenced datasets.</li><li>Read and apply window/level found in DICOM volumes.</li><li>Added support for Philips DWI datasets</li><li>Fixed loading of DICOM image from files containing special characters.</li></ul><br />
<br />
Image:20141116_SubjectHierarchyAnnouncement.png|Improved [[Documentation/Nightly/Modules/SubjectHierarchy|Subject hierarchy]] module for organizing and manipulating data loaded in Slicer.<ul><li>Highlight nodes in subject hierarchy referenced by DICOM</li><li>Added Transforms subject hierarchy plugin</li><li>Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]]. [http://www.na-mic.org/Bug/view.php?id=3163 #3163]</li><li>Added generic folder plugin to subject hierarchy</li><li>Subject hierarchy nodes automatically created for supported types</li><li>Added auto-delete subject hierarchy children to Application Settings </li><li>Added auto-create subject hierarchy option to Application Settings </li><li>Subject hierarchy tree headers show icons instead of text </li><li>Fixed subject hierarchy nodes creation when importing old scene [http://www.na-mic.org/Bug/view.php?id=3902 #3902]</li><li>Fixed volume visibility controls. [http://www.na-mic.org/Bug/view.php?id=3893 #3893]</li></ul><br />
<br />
<br />
</gallery><br />
<br />
= Slicer Training =<br />
<br />
The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of updated tutorials and data sets for training in the use of Slicer {{documentation/version}}. <br />
<br />
<br />
<gallery caption="New Tutorials" widths="250px" heights="150px" perrow="4"><br />
<br />
Image:2014-Slicer-Iowa-crop.png|This is an example of description {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
<br />
</gallery><br />
<br />
=Slicer Extensions=<br />
<br />
<gallery caption="New Extensions" widths="250px" heights="150px" perrow="4"><br />
<br />
Image:AnglePlanes Logo.png|[[Documentation/{{documentation/version}}/Extensions/AnglePlanes|AnglePlanes]] This Module is used to calculate the angle between two planes by using the normals {{new}}<br />
<br />
Image:Chest_Imaging_Platform.png|[http://www.chestimagingplatform.org/ Chest_Imaging_Platform] Chest Imaging Platform is an extension for quantitative CT imaging biomarkers for lung diseases {{new}}<br />
<br />
Image:DebuggingTools.png|[[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]] This extension contains various tools useful for developing and debugging modules {{new}}<br />
<br />
Image:SlicerExtension-DeveloperToolsForExtensions.png|[[Documentation/{{documentation/version}}/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] This extension offers different tools to help developers when they create Slicer extension {{new}}<br />
<br />
Image:DTI-Reg.png|[[Documentation/{{documentation/version}}/Extensions/DTI-Reg|DTI-Reg]] DTI-Reg is an extension that performs pair-wise DTI registration, using scalar FA map to drive the registration {{new}}<br />
<br />
Image:EasyClipLogo.png|[[Documentation/{{documentation/version}}/Extensions/EasyClip|EasyClip]] This Module is used to clip one or different 3D Models according to a predetermined plane {{new}}<br />
<br />
Image:GraphCutSegment.png|[http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] This is a segment extension using graph cut and star shape algorithm {{new}}<br />
<br />
Image:LumpNav.png|[https://github.com/SlicerIGT/LumpNav LumpNav] Breast tumor resection using tracked ultrasound and cautery {{new}}<br />
<br />
Image:MarginCalculator Logo2 128.png|[[Documentation/{{documentation/version}}/Extensions/MarginCalculator|MarginCalculator]] The Matlab Bridge extension allows running Matlab scripts as command-line interface (CLI) modules directly from 3D Slicer {{new}}<br />
<br />
Image:MeshStatisticsExtension.png|[[Documentation/{{documentation/version}}/Extensions/MeshStatistics|MeshStatistics]] Mesh Statistics allows users to compute descriptive statistics over specific and predefined regions {{new}}<br />
<br />
Image:Icon1.png|[[Documentation/{{documentation/version}}/Extensions/MeshToLabelMap|MeshToLabelMap]] This extension computes a label map from a 3D model {{new}}<br />
<br />
Image:PET-IndiC.png|[[Documentation/{{documentation/version}}/Extensions/PET-IndiC|PET-IndiC]] The PET-IndiC Extension allows for fast segmentation of regions of interest and calculation of quantitative indices {{new}}<br />
<br />
Image:DPetBrainQuantification.png|[http://gti-fing.github.io/SlicerPetSpectAnalysis/ PetSpectAnalysis] First Version of the Pet Spect Analysis Extension {{new}}<br />
<br />
Image:PETTumorSegmentationExtensionIcon.png|[[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PETTumorSegmentation]] Tumor and lymph node segmentation in PET scans {{new}}<br />
<br />
Image:PickAndPaintExtension.png|[[Documentation/{{documentation/version}}/Extensions/PickAndPaint|PickAndPaint]] Pick 'n Paint tool allows users to select ROIs on a reference model and to propagate it over different time point models {{new}}<br />
<br />
Image:Q3DC.png|[[Documentation/{{documentation/version}}/Extensions/Q3DC|Q3DC]] This extension contains one module of the same name {{new}}<br />
<br />
Image:ResampleDTIlogEuclidean-128x128-icon.png|[[Documentation/{{documentation/version}}/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] This resamples Diffusion Tensor Images (DTI) in the log-euclidean framework {{new}}<br />
<br />
Image:SlicerHeart Logo 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerHeart|SlicerHeart]] Modules for cardiac analysis and intervention planning and guidance {{new}}<br />
<br />
Image:SlicerProstate Logo 1.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerProstate|SlicerProstate]] SlicerProstate extension hosts various modules to facilitate processing and management of prostate image data, utilizing prostate images in image-guided interventions and development of the imaging biomarkers of the prostate cancer {{new}}<br />
<br />
Image:Slicer-Wasp.png|[https://github.com/Tomnl/Slicer-Wasp Slicer-Wasp] A module to perform a series of ITK watershed segmentation (without seeds) and then let the user create a label map out of selected components {{new}}<br />
<br />
Image:T1 Mapping Logo Resized.png|[[Documentation/{{documentation/version}}/Extensions/T1Mapping|T1Mapping]] T1 mapping estimates effective tissue parameter maps (T1) from multi-spectral FLASH MRI scans with different flip angles {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
</gallery><br />
<br />
== Improved Extensions in Slicer 4.5 ==<br />
<br />
* [http://www.nitrc.org/projects/abc ABC]<br />
* [[Documentation/{{documentation/version}}/Extensions/CMFreg|CMFreg]]<br />
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]]<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]]<br />
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetryAnalysis]]<br />
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]]<br />
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|MatlabBridge]]<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]]<br />
* [[Documentation/{{documentation/version}}/Extensions/NeedleFinder|NeedleFinder]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PETDICOMExtension]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]<br />
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]]<br />
* [[Documentation/{{documentation/version}}/Extensions/VolumeClip|VolumeClip]]<br />
<br />
== Extensions removed from Slicer 4.5 ==<br />
<br />
* houghTransformCLI: Removed by the original author because it was not needed anymore.<br />
<br />
== Extensions renamed ==<br />
<br />
* PyDevRemoteDebug -> [[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]]<br />
* MultidimData -> [[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]]<br />
* TrackerStabilizer -> [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Slicer-TrackerStabilizer]]<br />
* AirwaySegmentation -> [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Slicer-AirwaySegmentation]]<br />
<br />
= Other Improvements, Additions & Documentation =<br />
<br />
== Optimization ==<br />
* Added support for loading of large images on windows. <br />
* Reduced the memory footprint by fixing memory leaks<br />
* Sped up by 2x slice rendering when the volume is linearly transformed. <br />
* Improved reslicing speed of quasi-axis-aligned slices. <br />
* Sped up annotation ROI display about 10x faster (100ms to 10ms). <br />
* Improved tractography display performance. <br />
* Prevent viewers flickering when only few nodes are removed.<br />
* Improved performance of transform widget.<br />
<br />
== Transforms ==<br />
* Added support for copy/paste of linear transforms.<br />
* Support saving of any transform to a grid transform. <br />
* Addressed translation slider instability in rotate first mode. <br />
* Improved composite transform support. <br />
* Added support for thin plate spline transforms. <br />
* Changed default ITK bspline transform writing file format to ITKv4. <br />
* Addressed display issue for slice intersection display of non-linearly transformed model. <br />
* Made transforms module translate-rotate first icon nicer.<br />
<br />
== DICOM ==<br />
* Improved DICOM browser adding a right click menu allowing delting and exporting to disk patients/studies/series<br />
* Improved support for loading of DICOM referenced datasets.<br />
* Added support for DICOM private dictionary<br />
* Read and apply window/level found in DICOM volumes.<br />
* Added support for Philips DWI datasets<br />
* Fixed loading of DICOM image from files containing special characters.<br />
<br />
== Data processing ==<br />
* Added support for saving and loading of complex processing chain of CLI modules [http://www.na-mic.org/Bug/view.php?id=3240 #3240] [http://www.na-mic.org/Bug/view.php?id=3468 #3468]<br />
<br />
== CLI ==<br />
* Added support for transfer of fiducial file to/from CLI modules. <br />
* Added support for transfer of Hierarchy sub-scene to/from CLI modules. <br />
* Fixed loading multivolumes produced by CLI modules. <br />
<br />
== Usability ==<br />
* Built-in module categories and extensions categories are listed separately in module selector.<br />
* Allow multi-selection in subject hierarchy.<br />
* Generate high-resolution magnified screenshots for 3D view.<br />
<br />
== SubjectHierarchy ==<br />
* Highlight nodes in subject hierarchy referenced by DICOM <br />
* Added Transforms subject hierarchy plugin <br />
* Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]]. [http://www.na-mic.org/Bug/view.php?id=3163 #3163]<br />
* Added generic folder plugin to subject hierarchy <br />
* Subject hierarchy nodes automatically created for supported types <br />
* Added auto-delete subject hierarchy children to Application Settings <br />
* Added auto-create subject hierarchy option to Application Settings <br />
* Subject hierarchy tree headers show icons instead of text <br />
* Fixed subject hierarchy nodes creation when importing old scene [http://www.na-mic.org/Bug/view.php?id=3902 #3902]<br />
* Fixed volume visibility controls. [http://www.na-mic.org/Bug/view.php?id=3893 #3893]<br />
<br />
== Python scripting ==<br />
* Upgraded from Numpy 1.4.1 to NumPy 1.9.2<br />
* Upgraded from Python 2.7.3 to Python 2.7.10<br />
* Bundled nose python module into the Slicer package.<br />
* Added logging functions for Python. <br />
* Fixed VTKObservationMixin and added [[Documentation/Nightly/Developers/Python_scripting#How_can_I_access_callData_argument_in_a_VTK_object_observer_callback_function|documentation]].<br />
* Updated IOManager and DICOMWidgets to emit <code>newFileLoaded()</code>.<br />
* Added logging of Python console user input.<br />
* Added accessor for vertex points of models as numpy array. <br />
* Allow displayable manager to be introspected using python. <br />
<br />
== Editor ==<br />
* Warn user when GrowCut effect is attempted with unsupported image type. <br />
* Added ability to delete only the selected structure. <br />
* Ensure label map is updated each time a master volume is selected. <br />
* Improved threshold paint effect to have inclusive ranges [http://www.na-mic.org/Bug/view.php?id=4066 #4066]<br />
* Remember paint radius when effect are changed [http://www.na-mic.org/Bug/view.php?id=1853 #1853]<br />
* Reset editor interface when scene is closed. <br />
* Ensure a related merge volume is selected after a structure deleted.<br />
<br />
== Markups ==<br />
* Added measurements between fiducials in right click menu [http://www.na-mic.org/Bug/view.php?id=1898 #1898]<br />
* Added ability to refocus 3d cameras on a fiducial. [http://www.na-mic.org/Bug/view.php?id=3683 #3683]<br />
<br />
== LabelMapVolumeNode ==<br />
* TBD<br />
* Added labelmap node support to subject hierarchy <br />
* Improved CLI image widget type handling. <br />
<br />
== Slice viewers ==<br />
* Added control to adjust thickness for label map outlines [http://www.na-mic.org/Bug/view.php?id=2267 #2267]<br />
<br />
== DataProbe ==<br />
* Added magnified slice view into DataProbe panel. <br />
<br />
== SliceViewAnnotations ==<br />
* Added orientation marker to slice view annotations. <br />
* Improved integration of SliceViewAnnotations. [http://www.na-mic.org/Bug/view.php?id=3943 #3943]<br />
<br />
== OpenIGTLink ==<br />
* Improved support for POINT and POLYDATA messages. [http://www.na-mic.org/Bug/view.php?id=3875 #3875] [http://www.na-mic.org/Bug/view.php?id=3907 #3907]<br />
<br />
== DoubleArrays ==<br />
* Improved loading and saving of measurement files (.mcsv) <br />
<br />
== CastScalarVolume ==<br />
* Improved CastScalarVolume module to support input of type unsigned char, int or long. <br />
<br />
== SceneView ==<br />
* Improved management of data loaded between creation of SceneViews<br />
<br />
== Landmark ==<br />
* Added support for landmark refinement <br />
* Improved LandmarkRegistration plugin loader displaying message if plugin failed to be loaded.<br />
<br />
== MultiVolumeImporter ==<br />
* Fixed loading of MGH variable FA multivolume. <br />
<br />
== FiberBundleLabelSelect ==<br />
* Fixed ADD operation for ‘Label to include’. [http://www.na-mic.org/Bug/view.php?id=4025 #4025]<br />
* Added support for both VTK and VTP input files.<br />
<br />
== DTI support ==<br />
* Resolved multithread issue that caused errors with multiple b values. [http://www.na-mic.org/Bug/view.php?id=3977 #3977]<br />
* Fixed parallel/perpendicular diffusivity on glyphs, interactive seeding line display. [http://www.na-mic.org/Bug/view.php?id=3857 #3857]<br />
* Fixed displaying of Tensor properties and their ranges in Tractography display module for lines/tubes/glyphs [http://www.na-mic.org/Bug/view.php?id=3857 #3857]<br />
* Added logic for propagating color and opacity to fiber hierarchies. [http://www.na-mic.org/Bug/view.php?id=3925 #3925]<br />
* Added support for Fiber Hierarchies in the Models Module. [http://www.na-mic.org/Bug/view.php?id=3678 #3678]<br />
<br />
== VolumeRendering ==<br />
* Fixed volume rendering not visible when non-volume-rendered volume is frequently changing in the scene. <br />
* Ensure volume rendering is updated when volume geometry is modified. [http://www.na-mic.org/Bug/view.php?id=4023 #4023]<br />
<br />
== FiberTractMeasurements ==<br />
* TBD<br />
* Added CLI module FiberTractMeasurements allowing to XXXX supporting cluster aggregation.<br />
<br />
= For Developers =<br />
<br />
== Modules and Extensions ==<br />
<br />
* ExtensionWizard<br />
** Added "Enable developer mode" option to ExtensionWizard<br />
<br />
* SelfTests<br />
** Allow self tests to set a custom delay for message display<br />
<br />
* MRMLNodeComboBox<br />
** Allow qMRMLNodeComboBox base name setting for each node type <br />
** Added removeAttribute function to MRML node comboboxes and proxy model <br />
** Multiple node types can be created in qMRMLNodeComboBox <br />
** Support custom behavior for default actions. <br />
<br />
* MRML Scene introspection<br />
** Added node printself output to node inspector <br />
<br />
* Message logging<br />
** Added vtkInfoMacro<br />
<br />
* DICOM<br />
** Package additional DCMTK applications: echoscu, dsr2html, xml2dcm and xml2dsr<br />
<br />
* Markups<br />
** Signal end fiducial interaction in 3D <br />
** Add reusable simple markups widget <br />
<br />
* Module API<br />
** Extend module API with "widgetRepresentationCreationEnabled" property<br />
<br />
* Slicerlets<br />
** Allow slicelets and Slicer tests to handle log messages. <br />
<br />
* Units<br />
** Added extra units support: frequency, velocity and intensity.<br />
** Extended Units logic API adding GetDisplayCoefficient() and GetSIPrefixCoefficient() <br />
** Updated MRMLUnitNode to ensure value to string conversion account for precision. <br />
<br />
* SubjectHierarchy<br />
** Introduced adaptor classes facilitating implementation of python scripted subject hierarchy plugins. <br />
** Introduced autoDeleteSubjectHierarchyChildren property <br />
<br />
* Editor<br />
** Facilitate re-use of Editor python components in extension (LabelStructureListWidget in 043f398)<br />
** Updated EditUtil API adding function SetUseLabelOutline() to explicitly set label outline state on all Slice nodes<br />
<br />
== Slicer Core ==<br />
<br />
* IDE integration<br />
** Improve build targets organization in IDE that support folders.<br />
** VisualStudio: Do not build documentation when F7 is pressed.<br />
** Facilitate integration with python IDE allowing minimal 'slicer' module to be imported.<br />
<br />
* Build-system<br />
** Add support for Visual Studio 2013.<br />
** Update build system anticipating transition to modern CMake.<br />
** Update MacOSX packaging infrastructure anticipating the signing of package in future release.<br />
** Update code base anticipitating compliance with C++11.<br />
** Remove <code>Slicer_ITKV3_COMPATIBILITY</code> build option.<br />
** Add option <code>Slicer_USE_ITKPython</code> to turn on ITK Python wrapping.<br />
** Removed duplicated code using ITK version of MGHIO.<br />
<br />
* Python<br />
** Added support writing scripted modules and widgets as new-style Python classes. <br />
** Simplify scripted module introducing SlicerPythonCppAPI. <br />
** Introduced qSlicerScriptedUtils::executeFile() <br />
** Updated CTK to include new PythonQt C++/Python ownership tracking feature. <br />
** Import scripted module as python module to avoid module top-level variables to clobber each other. [http://www.na-mic.org/Bug/view.php?id=3549 #3549]<br />
<br />
* Platform support<br />
** Fix support for 32-bit build allowing use of Slicer on Surface tablet.<br />
<br />
* Packaging & Testing infrastructure<br />
** Capturing VTK errors/warnings during testing.<br />
** Update extension build system to report packaging error on CDash.<br />
<br />
* Rendering / Visualization<br />
** Add Slicer_VTK_RENDERING_BACKEND configure option<br />
<br />
* MRML<br />
** Add support in vtkMRMLNode for multiple references to the same node. <br />
** Introducing InvokeCustomModifiedEvent. <br />
<br />
* ApplicationLogic<br />
** Added function PropagateLabelVolumeSelection(), PropagateForegroundVolumeSelection() and PropagateBackgroundVolumeSelection()<br />
<br />
* VolumeRenderingLogic<br />
** Extend volume rendering logic API adding GetPresetByName function. <br />
<br />
* View management<br />
** Add qMRMLLayoutViewFactory <br />
** Add utility method to display node in only 1 view <br />
<br />
<br />
<gallery caption="Improved Toolkits" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:CTK-Logo.png|Moved from CTK [https://github.com/commontk/CTK/commit/f64b68a f64b68a] to [https://github.com/commontk/CTK/commit/1c97e54 1c97e54] (499 commits) <!-- git log --oneline f64b68acd717dab060db41e8bee3f0f30df1a58f...1c97e5426f898bc7d074e6122992d0dd12bab56b --no-merges | wc -l --><br />
<br />
Image:CTKApplauncher_Logo.png|Moved from CTKAppLauncher v0.1.11 to v0.1.14 (43 commits) <!-- git log --oneline v0.1.11..v0.1.14 --no-merges | wc -l --><br />
<br />
Image:ITK_logo.png|Moved from ITK v4.4.1 to v4.6.0 (1089 commits) <!-- git log --oneline v4.4.1..56fae27 --no-merges | wc -l --><br />
<br />
Image:OpenIGTLink-Logo.png|Moved from OpenIGTLink [https://github.com/openigtlink/OpenIGTLink/compare/66e272d...849b434 66e272d to 849b434] (53 commits) <!-- git log --no-merges --oneline 66e272d..849b434 | wc -l --><br />
<br />
Image:Qt-logo.png |Moved from Qt 4.7.4 to Qt 4.8.6<br />
<br />
Image:VTK_logo.png|Moved from VTK v5.10.1 to VTK v6.2.0 (5490 commits) <!-- git log --oneline v5.10.1..b55dad7 --no-merges | wc -l --><br />
<br />
</gallery><br />
<br />
== Looking at the Code Changes ==<br />
<br />
From a git checkout you can easily see the all the commits since the time of the 4.4.0 release:<br />
<br />
git log v4.4.0..HEAD<br />
<br />
To see a summary of your own commits, you could use something like:<br />
<br />
git log v4.4.0..HEAD --oneline --author=me<br />
<br />
see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.<br />
<br />
[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]<br />
<br />
= Related Projects =<br />
<gallery caption="" widths="250px" heights="150px" perrow="3"><br />
</gallery></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Announcements&diff=43201Documentation/Nightly/Announcements2015-11-02T16:05:26Z<p>Nicole: /* Editor */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
__NOTOC__<br />
<br />
<br />
<br />
{|width="100%"<br />
|align="center"|<br />
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]<br />
|}<br />
<br />
<br />
{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"<br />
|[[#Summary|Summary ]]<br />
|[[#What is 3D Slicer|What is 3D Slicer]]<br />
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]<br />
|[[#Slicer Training|Slicer Training]]<br />
|[[#Slicer Extensions|Slicer Extensions]]<br />
|[[#Other Improvements, Additions & Documentation|Other Improvements, Additions & Documentation]]<br />
|}<br />
<br />
= Summary = <br />
<br />
The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.<br />
<br />
* Slicer {{documentation/version}} introduces <br />
** An improved App Store, known as the Extension Manager, for adding plug-ins to Slicer. More than 80 plug-ins and packages of plug-ins are currently available.<br />
** Close to 150 feature improvements and bug fixes have resulted in improved performance and stability.<br />
** Improvements to many modules.<br />
<br />
* Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and the bug tracker. <br />
* Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.<br />
* The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of tutorials and data sets for training in the use of Slicer. <br />
<br />
[http://www.slicer.org slicer.org] is the portal to the application, training materials, and the development community.<br />
<br />
= What is 3D Slicer =<br />
{{:Documentation/{{documentation/version}}/Slicer}}<br />
<br />
= Slicer {{documentation/version}} Highlights =<br />
<br />
<gallery caption="New and Improved Modules" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:Grid3dVolume.png|Improved [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module with support for non-linear transforms, visualization of transforms in 2D and 3D, detailed transform properties view - '''[https://www.youtube.com/watch?v=kZUAfR0mqqI click here for demo video]'''.<ul><li>Added support for copy/paste of linear transforms</li><li>Support saving of any transform to a grid transform</li><li> Improved composite transform support</li><li>Added support for thin plate spline transforms</li><li>Addressed display issue for slice intersection display of non-linearly transformed model</li></ul><br />
<br />
Image:DICOM Screenshot.png |The user interface of the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module has been improved for a better usability.<ul><li>Improved DICOM browser adding a right click menu to allow deleting or exporting to disk at the patients/studies/series levels.</li><li>Added support for DICOM private dictionary.</li><li>Improved support for loading of DICOM referenced datasets.</li><li>Read and apply window/level found in DICOM volumes.</li><li>Added support for Philips DWI datasets</li><li>Fixed loading of DICOM image from files containing special characters.</li></ul><br />
<br />
Image:20141116_SubjectHierarchyAnnouncement.png|Improved [[Documentation/Nightly/Modules/SubjectHierarchy|Subject hierarchy]] module for organizing and manipulating data loaded in Slicer.<ul><li>Highlight nodes in subject hierarchy referenced by DICOM</li><li>Added Transforms subject hierarchy plugin</li><li>Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]]. [http://www.na-mic.org/Bug/view.php?id=3163 #3163]</li><li>Added generic folder plugin to subject hierarchy</li><li>Subject hierarchy nodes automatically created for supported types</li><li>Added auto-delete subject hierarchy children to Application Settings </li><li>Added auto-create subject hierarchy option to Application Settings </li><li>Subject hierarchy tree headers show icons instead of text </li><li>Fixed subject hierarchy nodes creation when importing old scene [http://www.na-mic.org/Bug/view.php?id=3902 #3902]</li><li>Fixed volume visibility controls. [http://www.na-mic.org/Bug/view.php?id=3893 #3893]</li></ul><br />
<br />
<br />
</gallery><br />
<br />
= Slicer Training =<br />
<br />
The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of updated tutorials and data sets for training in the use of Slicer {{documentation/version}}. <br />
<br />
<br />
<gallery caption="New Tutorials" widths="250px" heights="150px" perrow="4"><br />
<br />
Image:2014-Slicer-Iowa-crop.png|This is an example of description {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
<br />
</gallery><br />
<br />
=Slicer Extensions=<br />
<br />
<gallery caption="New Extensions" widths="250px" heights="150px" perrow="4"><br />
<br />
Image:AnglePlanes Logo.png|[[Documentation/{{documentation/version}}/Extensions/AnglePlanes|AnglePlanes]] This Module is used to calculate the angle between two planes by using the normals {{new}}<br />
<br />
Image:Chest_Imaging_Platform.png|[http://www.chestimagingplatform.org/ Chest_Imaging_Platform] Chest Imaging Platform is an extension for quantitative CT imaging biomarkers for lung diseases {{new}}<br />
<br />
Image:DebuggingTools.png|[[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]] This extension contains various tools useful for developing and debugging modules {{new}}<br />
<br />
Image:SlicerExtension-DeveloperToolsForExtensions.png|[[Documentation/{{documentation/version}}/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] This extension offers different tools to help developers when they create Slicer extension {{new}}<br />
<br />
Image:DTI-Reg.png|[[Documentation/{{documentation/version}}/Extensions/DTI-Reg|DTI-Reg]] DTI-Reg is an extension that performs pair-wise DTI registration, using scalar FA map to drive the registration {{new}}<br />
<br />
Image:EasyClipLogo.png|[[Documentation/{{documentation/version}}/Extensions/EasyClip|EasyClip]] This Module is used to clip one or different 3D Models according to a predetermined plane {{new}}<br />
<br />
Image:GraphCutSegment.png|[http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] This is a segment extension using graph cut and star shape algorithm {{new}}<br />
<br />
Image:LumpNav.png|[https://github.com/SlicerIGT/LumpNav LumpNav] Breast tumor resection using tracked ultrasound and cautery {{new}}<br />
<br />
Image:MarginCalculator Logo2 128.png|[[Documentation/{{documentation/version}}/Extensions/MarginCalculator|MarginCalculator]] The Matlab Bridge extension allows running Matlab scripts as command-line interface (CLI) modules directly from 3D Slicer {{new}}<br />
<br />
Image:MeshStatisticsExtension.png|[[Documentation/{{documentation/version}}/Extensions/MeshStatistics|MeshStatistics]] Mesh Statistics allows users to compute descriptive statistics over specific and predefined regions {{new}}<br />
<br />
Image:Icon1.png|[[Documentation/{{documentation/version}}/Extensions/MeshToLabelMap|MeshToLabelMap]] This extension computes a label map from a 3D model {{new}}<br />
<br />
Image:PET-IndiC.png|[[Documentation/{{documentation/version}}/Extensions/PET-IndiC|PET-IndiC]] The PET-IndiC Extension allows for fast segmentation of regions of interest and calculation of quantitative indices {{new}}<br />
<br />
Image:DPetBrainQuantification.png|[http://gti-fing.github.io/SlicerPetSpectAnalysis/ PetSpectAnalysis] First Version of the Pet Spect Analysis Extension {{new}}<br />
<br />
Image:PETTumorSegmentationExtensionIcon.png|[[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PETTumorSegmentation]] Tumor and lymph node segmentation in PET scans {{new}}<br />
<br />
Image:PickAndPaintExtension.png|[[Documentation/{{documentation/version}}/Extensions/PickAndPaint|PickAndPaint]] Pick 'n Paint tool allows users to select ROIs on a reference model and to propagate it over different time point models {{new}}<br />
<br />
Image:Q3DC.png|[[Documentation/{{documentation/version}}/Extensions/Q3DC|Q3DC]] This extension contains one module of the same name {{new}}<br />
<br />
Image:ResampleDTIlogEuclidean-128x128-icon.png|[[Documentation/{{documentation/version}}/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] This resamples Diffusion Tensor Images (DTI) in the log-euclidean framework {{new}}<br />
<br />
Image:SlicerHeart Logo 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerHeart|SlicerHeart]] Modules for cardiac analysis and intervention planning and guidance {{new}}<br />
<br />
Image:SlicerProstate Logo 1.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerProstate|SlicerProstate]] SlicerProstate extension hosts various modules to facilitate processing and management of prostate image data, utilizing prostate images in image-guided interventions and development of the imaging biomarkers of the prostate cancer {{new}}<br />
<br />
Image:Slicer-Wasp.png|[https://github.com/Tomnl/Slicer-Wasp Slicer-Wasp] A module to perform a series of ITK watershed segmentation (without seeds) and then let the user create a label map out of selected components {{new}}<br />
<br />
Image:T1 Mapping Logo Resized.png|[[Documentation/{{documentation/version}}/Extensions/T1Mapping|T1Mapping]] T1 mapping estimates effective tissue parameter maps (T1) from multi-spectral FLASH MRI scans with different flip angles {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
</gallery><br />
<br />
== Improved Extensions in Slicer 4.5 ==<br />
<br />
* [http://www.nitrc.org/projects/abc ABC]<br />
* [[Documentation/{{documentation/version}}/Extensions/CMFreg|CMFreg]]<br />
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]]<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]]<br />
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetryAnalysis]]<br />
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]]<br />
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|MatlabBridge]]<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]]<br />
* [[Documentation/{{documentation/version}}/Extensions/NeedleFinder|NeedleFinder]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PETDICOMExtension]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]<br />
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]]<br />
* [[Documentation/{{documentation/version}}/Extensions/VolumeClip|VolumeClip]]<br />
<br />
== Extensions removed from Slicer 4.5 ==<br />
<br />
* houghTransformCLI: Removed by the original author because it was not needed anymore.<br />
<br />
== Extensions renamed ==<br />
<br />
* PyDevRemoteDebug -> [[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]]<br />
* MultidimData -> [[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]]<br />
* TrackerStabilizer -> [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Slicer-TrackerStabilizer]]<br />
* AirwaySegmentation -> [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Slicer-AirwaySegmentation]]<br />
<br />
= Other Improvements, Additions & Documentation =<br />
<br />
== Optimization ==<br />
* Added support for loading of large images on windows. <br />
* Reduced the memory footprint by fixing memory leaks<br />
* Sped up by 2x slice rendering when the volume is linearly transformed. <br />
* Improved reslicing speed of quasi-axis-aligned slices. <br />
* Sped up annotation ROI display about 10x faster (100ms to 10ms). <br />
* Improved tractography display performance. <br />
* Prevent viewers flickering when only few nodes are removed.<br />
* Improved performance of transform widget.<br />
<br />
== Transforms ==<br />
* Added support for copy/paste of linear transforms.<br />
* Support saving of any transform to a grid transform. <br />
* Addressed translation slider instability in rotate first mode. <br />
* Improved composite transform support. <br />
* Added support for thin plate spline transforms. <br />
* Changed default ITK bspline transform writing file format to ITKv4. <br />
* Addressed display issue for slice intersection display of non-linearly transformed model. <br />
* Made transforms module translate-rotate first icon nicer.<br />
<br />
== DICOM ==<br />
* Improved DICOM browser adding a right click menu allowing delting and exporting to disk patients/studies/series<br />
* Improved support for loading of DICOM referenced datasets.<br />
* Added support for DICOM private dictionary<br />
* Read and apply window/level found in DICOM volumes.<br />
* Added support for Philips DWI datasets<br />
* Fixed loading of DICOM image from files containing special characters.<br />
<br />
== Data processing ==<br />
* Added support for saving and loading of complex processing chain of CLI modules [http://www.na-mic.org/Bug/view.php?id=3240 #3240] [http://www.na-mic.org/Bug/view.php?id=3468 #3468]<br />
<br />
== CLI ==<br />
* Added support for transfer of fiducial file to/from CLI modules. <br />
* Added support for transfer of Hierarchy sub-scene to/from CLI modules. <br />
* Fixed loading multivolumes produced by CLI modules. <br />
<br />
== Usability ==<br />
* Built-in module categories and extensions categories are listed separately in module selector.<br />
* Allow multi-selection in subject hierarchy.<br />
* Generate high-resolution magnified screenshots for 3D view.<br />
<br />
== SubjectHierarchy ==<br />
* Highlight nodes in subject hierarchy referenced by DICOM <br />
* Added Transforms subject hierarchy plugin <br />
* Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]]. [http://www.na-mic.org/Bug/view.php?id=3163 #3163]<br />
* Added generic folder plugin to subject hierarchy <br />
* Subject hierarchy nodes automatically created for supported types <br />
* Added auto-delete subject hierarchy children to Application Settings <br />
* Added auto-create subject hierarchy option to Application Settings <br />
* Subject hierarchy tree headers show icons instead of text <br />
* Fixed subject hierarchy nodes creation when importing old scene [http://www.na-mic.org/Bug/view.php?id=3902 #3902]<br />
* Fixed volume visibility controls. [http://www.na-mic.org/Bug/view.php?id=3893 #3893]<br />
<br />
== Python scripting ==<br />
* Upgraded from Numpy 1.4.1 to NumPy 1.9.2<br />
* Upgraded from Python 2.7.3 to Python 2.7.10<br />
* Bundled nose python module into the Slicer package.<br />
* Added logging functions for Python. <br />
* Fixed VTKObservationMixin and added [[Documentation/Nightly/Developers/Python_scripting#How_can_I_access_callData_argument_in_a_VTK_object_observer_callback_function|documentation]].<br />
* Updated IOManager and DICOMWidgets to emit <code>newFileLoaded()</code>.<br />
* Added logging of Python console user input.<br />
* Added accessor for vertex points of models as numpy array. <br />
* Allow displayable manager to be introspected using python. <br />
<br />
== Editor ==<br />
* Warn user when GrowCut effect is attempted with unsupported image type. <br />
* Added ability to delete only the selected structure. <br />
* Ensure label map is updated each time a master volume is selected. <br />
* Improved threshold paint effect to have inclusive ranges [http://www.na-mic.org/Bug/view.php?id=4066 #4066]<br />
* Remember paint radius when effect are changed [http://www.na-mic.org/Bug/view.php?id=1853 #1853]<br />
* Reset editor interface when scene is closed. <br />
* Ensure a related merge volume is selected after a structure deleted.<br />
<br />
== Markups ==<br />
* Added ability to refocus 3d cameras on a fiducial. [http://www.na-mic.org/Bug/view.php?id=3683 #3683]<br />
<br />
== LabelMapVolumeNode ==<br />
* TBD<br />
* Added labelmap node support to subject hierarchy <br />
* Improved CLI image widget type handling. <br />
<br />
== Slice viewers ==<br />
* Added control to adjust thickness for label map outlines [http://www.na-mic.org/Bug/view.php?id=2267 #2267]<br />
<br />
== DataProbe ==<br />
* Added magnified slice view into DataProbe panel. <br />
<br />
== SliceViewAnnotations ==<br />
* Added orientation marker to slice view annotations. <br />
* Improved integration of SliceViewAnnotations. [http://www.na-mic.org/Bug/view.php?id=3943 #3943]<br />
<br />
== OpenIGTLink ==<br />
* Improved support for POINT and POLYDATA messages. [http://www.na-mic.org/Bug/view.php?id=3875 #3875] [http://www.na-mic.org/Bug/view.php?id=3907 #3907]<br />
<br />
== DoubleArrays ==<br />
* Improved loading and saving of measurement files (.mcsv) <br />
<br />
== CastScalarVolume ==<br />
* Improved CastScalarVolume module to support input of type unsigned char, int or long. <br />
<br />
== SceneView ==<br />
* Improved management of data loaded between creation of SceneViews<br />
<br />
== Landmark ==<br />
* Added support for landmark refinement <br />
* Improved LandmarkRegistration plugin loader displaying message if plugin failed to be loaded.<br />
<br />
== MultiVolumeImporter ==<br />
* Fixed loading of MGH variable FA multivolume. <br />
<br />
== FiberBundleLabelSelect ==<br />
* Fixed ADD operation for ‘Label to include’. [http://www.na-mic.org/Bug/view.php?id=4025 #4025]<br />
* Added support for both VTK and VTP input files.<br />
<br />
== DTI support ==<br />
* Resolved multithread issue that caused errors with multiple b values. [http://www.na-mic.org/Bug/view.php?id=3977 #3977]<br />
* Fixed parallel/perpendicular diffusivity on glyphs, interactive seeding line display. [http://www.na-mic.org/Bug/view.php?id=3857 #3857]<br />
* Fixed displaying of Tensor properties and their ranges in Tractography display module for lines/tubes/glyphs [http://www.na-mic.org/Bug/view.php?id=3857 #3857]<br />
* Added logic for propagating color and opacity to fiber hierarchies. [http://www.na-mic.org/Bug/view.php?id=3925 #3925]<br />
* Added support for Fiber Hierarchies in the Models Module. [http://www.na-mic.org/Bug/view.php?id=3678 #3678]<br />
<br />
== VolumeRendering ==<br />
* Fixed volume rendering not visible when non-volume-rendered volume is frequently changing in the scene. <br />
* Ensure volume rendering is updated when volume geometry is modified. [http://www.na-mic.org/Bug/view.php?id=4023 #4023]<br />
<br />
== FiberTractMeasurements ==<br />
* TBD<br />
* Added CLI module FiberTractMeasurements allowing to XXXX supporting cluster aggregation.<br />
<br />
= For Developers =<br />
<br />
== Modules and Extensions ==<br />
<br />
* ExtensionWizard<br />
** Added "Enable developer mode" option to ExtensionWizard<br />
<br />
* SelfTests<br />
** Allow self tests to set a custom delay for message display<br />
<br />
* MRMLNodeComboBox<br />
** Allow qMRMLNodeComboBox base name setting for each node type <br />
** Added removeAttribute function to MRML node comboboxes and proxy model <br />
** Multiple node types can be created in qMRMLNodeComboBox <br />
** Support custom behavior for default actions. <br />
<br />
* MRML Scene introspection<br />
** Added node printself output to node inspector <br />
<br />
* Message logging<br />
** Added vtkInfoMacro<br />
<br />
* DICOM<br />
** Package additional DCMTK applications: echoscu, dsr2html, xml2dcm and xml2dsr<br />
<br />
* Markups<br />
** Signal end fiducial interaction in 3D <br />
** Add reusable simple markups widget <br />
<br />
* Module API<br />
** Extend module API with "widgetRepresentationCreationEnabled" property<br />
<br />
* Slicerlets<br />
** Allow slicelets and Slicer tests to handle log messages. <br />
<br />
* Units<br />
** Added extra units support: frequency, velocity and intensity.<br />
** Extended Units logic API adding GetDisplayCoefficient() and GetSIPrefixCoefficient() <br />
** Updated MRMLUnitNode to ensure value to string conversion account for precision. <br />
<br />
* SubjectHierarchy<br />
** Introduced adaptor classes facilitating implementation of python scripted subject hierarchy plugins. <br />
** Introduced autoDeleteSubjectHierarchyChildren property <br />
<br />
* Editor<br />
** Facilitate re-use of Editor python components in extension (LabelStructureListWidget in 043f398)<br />
** Updated EditUtil API adding function SetUseLabelOutline() to explicitly set label outline state on all Slice nodes<br />
<br />
== Slicer Core ==<br />
<br />
* IDE integration<br />
** Improve build targets organization in IDE that support folders.<br />
** VisualStudio: Do not build documentation when F7 is pressed.<br />
** Facilitate integration with python IDE allowing minimal 'slicer' module to be imported.<br />
<br />
* Build-system<br />
** Add support for Visual Studio 2013.<br />
** Update build system anticipating transition to modern CMake.<br />
** Update MacOSX packaging infrastructure anticipating the signing of package in future release.<br />
** Update code base anticipitating compliance with C++11.<br />
** Remove <code>Slicer_ITKV3_COMPATIBILITY</code> build option.<br />
** Add option <code>Slicer_USE_ITKPython</code> to turn on ITK Python wrapping.<br />
** Removed duplicated code using ITK version of MGHIO.<br />
<br />
* Python<br />
** Added support writing scripted modules and widgets as new-style Python classes. <br />
** Simplify scripted module introducing SlicerPythonCppAPI. <br />
** Introduced qSlicerScriptedUtils::executeFile() <br />
** Updated CTK to include new PythonQt C++/Python ownership tracking feature. <br />
** Import scripted module as python module to avoid module top-level variables to clobber each other. [http://www.na-mic.org/Bug/view.php?id=3549 #3549]<br />
<br />
* Platform support<br />
** Fix support for 32-bit build allowing use of Slicer on Surface tablet.<br />
<br />
* Packaging & Testing infrastructure<br />
** Capturing VTK errors/warnings during testing.<br />
** Update extension build system to report packaging error on CDash.<br />
<br />
* Rendering / Visualization<br />
** Add Slicer_VTK_RENDERING_BACKEND configure option<br />
<br />
* MRML<br />
** Add support in vtkMRMLNode for multiple references to the same node. <br />
** Introducing InvokeCustomModifiedEvent. <br />
<br />
* ApplicationLogic<br />
** Added function PropagateLabelVolumeSelection(), PropagateForegroundVolumeSelection() and PropagateBackgroundVolumeSelection()<br />
<br />
* VolumeRenderingLogic<br />
** Extend volume rendering logic API adding GetPresetByName function. <br />
<br />
* View management<br />
** Add qMRMLLayoutViewFactory <br />
** Add utility method to display node in only 1 view <br />
<br />
<br />
<gallery caption="Improved Toolkits" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:CTK-Logo.png|Moved from CTK [https://github.com/commontk/CTK/commit/f64b68a f64b68a] to [https://github.com/commontk/CTK/commit/1c97e54 1c97e54] (499 commits) <!-- git log --oneline f64b68acd717dab060db41e8bee3f0f30df1a58f...1c97e5426f898bc7d074e6122992d0dd12bab56b --no-merges | wc -l --><br />
<br />
Image:CTKApplauncher_Logo.png|Moved from CTKAppLauncher v0.1.11 to v0.1.14 (43 commits) <!-- git log --oneline v0.1.11..v0.1.14 --no-merges | wc -l --><br />
<br />
Image:ITK_logo.png|Moved from ITK v4.4.1 to v4.6.0 (1089 commits) <!-- git log --oneline v4.4.1..56fae27 --no-merges | wc -l --><br />
<br />
Image:OpenIGTLink-Logo.png|Moved from OpenIGTLink [https://github.com/openigtlink/OpenIGTLink/compare/66e272d...849b434 66e272d to 849b434] (53 commits) <!-- git log --no-merges --oneline 66e272d..849b434 | wc -l --><br />
<br />
Image:Qt-logo.png |Moved from Qt 4.7.4 to Qt 4.8.6<br />
<br />
Image:VTK_logo.png|Moved from VTK v5.10.1 to VTK v6.2.0 (5490 commits) <!-- git log --oneline v5.10.1..b55dad7 --no-merges | wc -l --><br />
<br />
</gallery><br />
<br />
== Looking at the Code Changes ==<br />
<br />
From a git checkout you can easily see the all the commits since the time of the 4.4.0 release:<br />
<br />
git log v4.4.0..HEAD<br />
<br />
To see a summary of your own commits, you could use something like:<br />
<br />
git log v4.4.0..HEAD --oneline --author=me<br />
<br />
see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.<br />
<br />
[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]<br />
<br />
= Related Projects =<br />
<gallery caption="" widths="250px" heights="150px" perrow="3"><br />
</gallery></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Announcements&diff=43200Documentation/Nightly/Announcements2015-11-02T16:04:46Z<p>Nicole: /* DICOM */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
__NOTOC__<br />
<br />
<br />
<br />
{|width="100%"<br />
|align="center"|<br />
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]<br />
|}<br />
<br />
<br />
{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"<br />
|[[#Summary|Summary ]]<br />
|[[#What is 3D Slicer|What is 3D Slicer]]<br />
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]<br />
|[[#Slicer Training|Slicer Training]]<br />
|[[#Slicer Extensions|Slicer Extensions]]<br />
|[[#Other Improvements, Additions & Documentation|Other Improvements, Additions & Documentation]]<br />
|}<br />
<br />
= Summary = <br />
<br />
The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.<br />
<br />
* Slicer {{documentation/version}} introduces <br />
** An improved App Store, known as the Extension Manager, for adding plug-ins to Slicer. More than 80 plug-ins and packages of plug-ins are currently available.<br />
** Close to 150 feature improvements and bug fixes have resulted in improved performance and stability.<br />
** Improvements to many modules.<br />
<br />
* Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and the bug tracker. <br />
* Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.<br />
* The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of tutorials and data sets for training in the use of Slicer. <br />
<br />
[http://www.slicer.org slicer.org] is the portal to the application, training materials, and the development community.<br />
<br />
= What is 3D Slicer =<br />
{{:Documentation/{{documentation/version}}/Slicer}}<br />
<br />
= Slicer {{documentation/version}} Highlights =<br />
<br />
<gallery caption="New and Improved Modules" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:Grid3dVolume.png|Improved [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module with support for non-linear transforms, visualization of transforms in 2D and 3D, detailed transform properties view - '''[https://www.youtube.com/watch?v=kZUAfR0mqqI click here for demo video]'''.<ul><li>Added support for copy/paste of linear transforms</li><li>Support saving of any transform to a grid transform</li><li> Improved composite transform support</li><li>Added support for thin plate spline transforms</li><li>Addressed display issue for slice intersection display of non-linearly transformed model</li></ul><br />
<br />
Image:DICOM Screenshot.png |The user interface of the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module has been improved for a better usability.<ul><li>Improved DICOM browser adding a right click menu to allow deleting or exporting to disk at the patients/studies/series levels.</li><li>Added support for DICOM private dictionary.</li><li>Improved support for loading of DICOM referenced datasets.</li><li>Read and apply window/level found in DICOM volumes.</li><li>Added support for Philips DWI datasets</li><li>Fixed loading of DICOM image from files containing special characters.</li></ul><br />
<br />
Image:20141116_SubjectHierarchyAnnouncement.png|Improved [[Documentation/Nightly/Modules/SubjectHierarchy|Subject hierarchy]] module for organizing and manipulating data loaded in Slicer.<ul><li>Highlight nodes in subject hierarchy referenced by DICOM</li><li>Added Transforms subject hierarchy plugin</li><li>Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]]. [http://www.na-mic.org/Bug/view.php?id=3163 #3163]</li><li>Added generic folder plugin to subject hierarchy</li><li>Subject hierarchy nodes automatically created for supported types</li><li>Added auto-delete subject hierarchy children to Application Settings </li><li>Added auto-create subject hierarchy option to Application Settings </li><li>Subject hierarchy tree headers show icons instead of text </li><li>Fixed subject hierarchy nodes creation when importing old scene [http://www.na-mic.org/Bug/view.php?id=3902 #3902]</li><li>Fixed volume visibility controls. [http://www.na-mic.org/Bug/view.php?id=3893 #3893]</li></ul><br />
<br />
<br />
</gallery><br />
<br />
= Slicer Training =<br />
<br />
The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of updated tutorials and data sets for training in the use of Slicer {{documentation/version}}. <br />
<br />
<br />
<gallery caption="New Tutorials" widths="250px" heights="150px" perrow="4"><br />
<br />
Image:2014-Slicer-Iowa-crop.png|This is an example of description {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
<br />
</gallery><br />
<br />
=Slicer Extensions=<br />
<br />
<gallery caption="New Extensions" widths="250px" heights="150px" perrow="4"><br />
<br />
Image:AnglePlanes Logo.png|[[Documentation/{{documentation/version}}/Extensions/AnglePlanes|AnglePlanes]] This Module is used to calculate the angle between two planes by using the normals {{new}}<br />
<br />
Image:Chest_Imaging_Platform.png|[http://www.chestimagingplatform.org/ Chest_Imaging_Platform] Chest Imaging Platform is an extension for quantitative CT imaging biomarkers for lung diseases {{new}}<br />
<br />
Image:DebuggingTools.png|[[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]] This extension contains various tools useful for developing and debugging modules {{new}}<br />
<br />
Image:SlicerExtension-DeveloperToolsForExtensions.png|[[Documentation/{{documentation/version}}/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] This extension offers different tools to help developers when they create Slicer extension {{new}}<br />
<br />
Image:DTI-Reg.png|[[Documentation/{{documentation/version}}/Extensions/DTI-Reg|DTI-Reg]] DTI-Reg is an extension that performs pair-wise DTI registration, using scalar FA map to drive the registration {{new}}<br />
<br />
Image:EasyClipLogo.png|[[Documentation/{{documentation/version}}/Extensions/EasyClip|EasyClip]] This Module is used to clip one or different 3D Models according to a predetermined plane {{new}}<br />
<br />
Image:GraphCutSegment.png|[http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] This is a segment extension using graph cut and star shape algorithm {{new}}<br />
<br />
Image:LumpNav.png|[https://github.com/SlicerIGT/LumpNav LumpNav] Breast tumor resection using tracked ultrasound and cautery {{new}}<br />
<br />
Image:MarginCalculator Logo2 128.png|[[Documentation/{{documentation/version}}/Extensions/MarginCalculator|MarginCalculator]] The Matlab Bridge extension allows running Matlab scripts as command-line interface (CLI) modules directly from 3D Slicer {{new}}<br />
<br />
Image:MeshStatisticsExtension.png|[[Documentation/{{documentation/version}}/Extensions/MeshStatistics|MeshStatistics]] Mesh Statistics allows users to compute descriptive statistics over specific and predefined regions {{new}}<br />
<br />
Image:Icon1.png|[[Documentation/{{documentation/version}}/Extensions/MeshToLabelMap|MeshToLabelMap]] This extension computes a label map from a 3D model {{new}}<br />
<br />
Image:PET-IndiC.png|[[Documentation/{{documentation/version}}/Extensions/PET-IndiC|PET-IndiC]] The PET-IndiC Extension allows for fast segmentation of regions of interest and calculation of quantitative indices {{new}}<br />
<br />
Image:DPetBrainQuantification.png|[http://gti-fing.github.io/SlicerPetSpectAnalysis/ PetSpectAnalysis] First Version of the Pet Spect Analysis Extension {{new}}<br />
<br />
Image:PETTumorSegmentationExtensionIcon.png|[[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PETTumorSegmentation]] Tumor and lymph node segmentation in PET scans {{new}}<br />
<br />
Image:PickAndPaintExtension.png|[[Documentation/{{documentation/version}}/Extensions/PickAndPaint|PickAndPaint]] Pick 'n Paint tool allows users to select ROIs on a reference model and to propagate it over different time point models {{new}}<br />
<br />
Image:Q3DC.png|[[Documentation/{{documentation/version}}/Extensions/Q3DC|Q3DC]] This extension contains one module of the same name {{new}}<br />
<br />
Image:ResampleDTIlogEuclidean-128x128-icon.png|[[Documentation/{{documentation/version}}/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] This resamples Diffusion Tensor Images (DTI) in the log-euclidean framework {{new}}<br />
<br />
Image:SlicerHeart Logo 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerHeart|SlicerHeart]] Modules for cardiac analysis and intervention planning and guidance {{new}}<br />
<br />
Image:SlicerProstate Logo 1.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerProstate|SlicerProstate]] SlicerProstate extension hosts various modules to facilitate processing and management of prostate image data, utilizing prostate images in image-guided interventions and development of the imaging biomarkers of the prostate cancer {{new}}<br />
<br />
Image:Slicer-Wasp.png|[https://github.com/Tomnl/Slicer-Wasp Slicer-Wasp] A module to perform a series of ITK watershed segmentation (without seeds) and then let the user create a label map out of selected components {{new}}<br />
<br />
Image:T1 Mapping Logo Resized.png|[[Documentation/{{documentation/version}}/Extensions/T1Mapping|T1Mapping]] T1 mapping estimates effective tissue parameter maps (T1) from multi-spectral FLASH MRI scans with different flip angles {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
</gallery><br />
<br />
== Improved Extensions in Slicer 4.5 ==<br />
<br />
* [http://www.nitrc.org/projects/abc ABC]<br />
* [[Documentation/{{documentation/version}}/Extensions/CMFreg|CMFreg]]<br />
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]]<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]]<br />
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetryAnalysis]]<br />
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]]<br />
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|MatlabBridge]]<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]]<br />
* [[Documentation/{{documentation/version}}/Extensions/NeedleFinder|NeedleFinder]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PETDICOMExtension]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]<br />
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]]<br />
* [[Documentation/{{documentation/version}}/Extensions/VolumeClip|VolumeClip]]<br />
<br />
== Extensions removed from Slicer 4.5 ==<br />
<br />
* houghTransformCLI: Removed by the original author because it was not needed anymore.<br />
<br />
== Extensions renamed ==<br />
<br />
* PyDevRemoteDebug -> [[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]]<br />
* MultidimData -> [[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]]<br />
* TrackerStabilizer -> [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Slicer-TrackerStabilizer]]<br />
* AirwaySegmentation -> [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Slicer-AirwaySegmentation]]<br />
<br />
= Other Improvements, Additions & Documentation =<br />
<br />
== Optimization ==<br />
* Added support for loading of large images on windows. <br />
* Reduced the memory footprint by fixing memory leaks<br />
* Sped up by 2x slice rendering when the volume is linearly transformed. <br />
* Improved reslicing speed of quasi-axis-aligned slices. <br />
* Sped up annotation ROI display about 10x faster (100ms to 10ms). <br />
* Improved tractography display performance. <br />
* Prevent viewers flickering when only few nodes are removed.<br />
* Improved performance of transform widget.<br />
<br />
== Transforms ==<br />
* Added support for copy/paste of linear transforms.<br />
* Support saving of any transform to a grid transform. <br />
* Addressed translation slider instability in rotate first mode. <br />
* Improved composite transform support. <br />
* Added support for thin plate spline transforms. <br />
* Changed default ITK bspline transform writing file format to ITKv4. <br />
* Addressed display issue for slice intersection display of non-linearly transformed model. <br />
* Made transforms module translate-rotate first icon nicer.<br />
<br />
== DICOM ==<br />
* Improved DICOM browser adding a right click menu allowing delting and exporting to disk patients/studies/series<br />
* Improved support for loading of DICOM referenced datasets.<br />
* Added support for DICOM private dictionary<br />
* Read and apply window/level found in DICOM volumes.<br />
* Added support for Philips DWI datasets<br />
* Fixed loading of DICOM image from files containing special characters.<br />
<br />
== Data processing ==<br />
* Added support for saving and loading of complex processing chain of CLI modules [http://www.na-mic.org/Bug/view.php?id=3240 #3240] [http://www.na-mic.org/Bug/view.php?id=3468 #3468]<br />
<br />
== CLI ==<br />
* Added support for transfer of fiducial file to/from CLI modules. <br />
* Added support for transfer of Hierarchy sub-scene to/from CLI modules. <br />
* Fixed loading multivolumes produced by CLI modules. <br />
<br />
== Usability ==<br />
* Built-in module categories and extensions categories are listed separately in module selector.<br />
* Allow multi-selection in subject hierarchy.<br />
* Generate high-resolution magnified screenshots for 3D view.<br />
<br />
== SubjectHierarchy ==<br />
* Highlight nodes in subject hierarchy referenced by DICOM <br />
* Added Transforms subject hierarchy plugin <br />
* Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]]. [http://www.na-mic.org/Bug/view.php?id=3163 #3163]<br />
* Added generic folder plugin to subject hierarchy <br />
* Subject hierarchy nodes automatically created for supported types <br />
* Added auto-delete subject hierarchy children to Application Settings <br />
* Added auto-create subject hierarchy option to Application Settings <br />
* Subject hierarchy tree headers show icons instead of text <br />
* Fixed subject hierarchy nodes creation when importing old scene [http://www.na-mic.org/Bug/view.php?id=3902 #3902]<br />
* Fixed volume visibility controls. [http://www.na-mic.org/Bug/view.php?id=3893 #3893]<br />
<br />
== Python scripting ==<br />
* Upgraded from Numpy 1.4.1 to NumPy 1.9.2<br />
* Upgraded from Python 2.7.3 to Python 2.7.10<br />
* Bundled nose python module into the Slicer package.<br />
* Added logging functions for Python. <br />
* Fixed VTKObservationMixin and added [[Documentation/Nightly/Developers/Python_scripting#How_can_I_access_callData_argument_in_a_VTK_object_observer_callback_function|documentation]].<br />
* Updated IOManager and DICOMWidgets to emit <code>newFileLoaded()</code>.<br />
* Added logging of Python console user input.<br />
* Added accessor for vertex points of models as numpy array. <br />
* Allow displayable manager to be introspected using python. <br />
<br />
== Editor ==<br />
* Warn user when GrowCut effect is attempted with unsupported image type. <br />
* Added ability to delete only the selected structure. <br />
* Ensure label map is updated each time a master volume is selected. <br />
* Improved threshold paint effect to have inclusive ranges [http://www.na-mic.org/Bug/view.php?id=4066 #4066]<br />
* Remember pain radius when effect are changed [http://www.na-mic.org/Bug/view.php?id=1853 #1853]<br />
* Reset editor interface when scene is closed. <br />
* Ensure a related merge volume is selected after a structure deleted. <br />
<br />
== Markups ==<br />
* Added ability to refocus 3d cameras on a fiducial. [http://www.na-mic.org/Bug/view.php?id=3683 #3683]<br />
<br />
== LabelMapVolumeNode ==<br />
* TBD<br />
* Added labelmap node support to subject hierarchy <br />
* Improved CLI image widget type handling. <br />
<br />
== Slice viewers ==<br />
* Added control to adjust thickness for label map outlines [http://www.na-mic.org/Bug/view.php?id=2267 #2267]<br />
<br />
== DataProbe ==<br />
* Added magnified slice view into DataProbe panel. <br />
<br />
== SliceViewAnnotations ==<br />
* Added orientation marker to slice view annotations. <br />
* Improved integration of SliceViewAnnotations. [http://www.na-mic.org/Bug/view.php?id=3943 #3943]<br />
<br />
== OpenIGTLink ==<br />
* Improved support for POINT and POLYDATA messages. [http://www.na-mic.org/Bug/view.php?id=3875 #3875] [http://www.na-mic.org/Bug/view.php?id=3907 #3907]<br />
<br />
== DoubleArrays ==<br />
* Improved loading and saving of measurement files (.mcsv) <br />
<br />
== CastScalarVolume ==<br />
* Improved CastScalarVolume module to support input of type unsigned char, int or long. <br />
<br />
== SceneView ==<br />
* Improved management of data loaded between creation of SceneViews<br />
<br />
== Landmark ==<br />
* Added support for landmark refinement <br />
* Improved LandmarkRegistration plugin loader displaying message if plugin failed to be loaded.<br />
<br />
== MultiVolumeImporter ==<br />
* Fixed loading of MGH variable FA multivolume. <br />
<br />
== FiberBundleLabelSelect ==<br />
* Fixed ADD operation for ‘Label to include’. [http://www.na-mic.org/Bug/view.php?id=4025 #4025]<br />
* Added support for both VTK and VTP input files.<br />
<br />
== DTI support ==<br />
* Resolved multithread issue that caused errors with multiple b values. [http://www.na-mic.org/Bug/view.php?id=3977 #3977]<br />
* Fixed parallel/perpendicular diffusivity on glyphs, interactive seeding line display. [http://www.na-mic.org/Bug/view.php?id=3857 #3857]<br />
* Fixed displaying of Tensor properties and their ranges in Tractography display module for lines/tubes/glyphs [http://www.na-mic.org/Bug/view.php?id=3857 #3857]<br />
* Added logic for propagating color and opacity to fiber hierarchies. [http://www.na-mic.org/Bug/view.php?id=3925 #3925]<br />
* Added support for Fiber Hierarchies in the Models Module. [http://www.na-mic.org/Bug/view.php?id=3678 #3678]<br />
<br />
== VolumeRendering ==<br />
* Fixed volume rendering not visible when non-volume-rendered volume is frequently changing in the scene. <br />
* Ensure volume rendering is updated when volume geometry is modified. [http://www.na-mic.org/Bug/view.php?id=4023 #4023]<br />
<br />
== FiberTractMeasurements ==<br />
* TBD<br />
* Added CLI module FiberTractMeasurements allowing to XXXX supporting cluster aggregation.<br />
<br />
= For Developers =<br />
<br />
== Modules and Extensions ==<br />
<br />
* ExtensionWizard<br />
** Added "Enable developer mode" option to ExtensionWizard<br />
<br />
* SelfTests<br />
** Allow self tests to set a custom delay for message display<br />
<br />
* MRMLNodeComboBox<br />
** Allow qMRMLNodeComboBox base name setting for each node type <br />
** Added removeAttribute function to MRML node comboboxes and proxy model <br />
** Multiple node types can be created in qMRMLNodeComboBox <br />
** Support custom behavior for default actions. <br />
<br />
* MRML Scene introspection<br />
** Added node printself output to node inspector <br />
<br />
* Message logging<br />
** Added vtkInfoMacro<br />
<br />
* DICOM<br />
** Package additional DCMTK applications: echoscu, dsr2html, xml2dcm and xml2dsr<br />
<br />
* Markups<br />
** Signal end fiducial interaction in 3D <br />
** Add reusable simple markups widget <br />
<br />
* Module API<br />
** Extend module API with "widgetRepresentationCreationEnabled" property<br />
<br />
* Slicerlets<br />
** Allow slicelets and Slicer tests to handle log messages. <br />
<br />
* Units<br />
** Added extra units support: frequency, velocity and intensity.<br />
** Extended Units logic API adding GetDisplayCoefficient() and GetSIPrefixCoefficient() <br />
** Updated MRMLUnitNode to ensure value to string conversion account for precision. <br />
<br />
* SubjectHierarchy<br />
** Introduced adaptor classes facilitating implementation of python scripted subject hierarchy plugins. <br />
** Introduced autoDeleteSubjectHierarchyChildren property <br />
<br />
* Editor<br />
** Facilitate re-use of Editor python components in extension (LabelStructureListWidget in 043f398)<br />
** Updated EditUtil API adding function SetUseLabelOutline() to explicitly set label outline state on all Slice nodes<br />
<br />
== Slicer Core ==<br />
<br />
* IDE integration<br />
** Improve build targets organization in IDE that support folders.<br />
** VisualStudio: Do not build documentation when F7 is pressed.<br />
** Facilitate integration with python IDE allowing minimal 'slicer' module to be imported.<br />
<br />
* Build-system<br />
** Add support for Visual Studio 2013.<br />
** Update build system anticipating transition to modern CMake.<br />
** Update MacOSX packaging infrastructure anticipating the signing of package in future release.<br />
** Update code base anticipitating compliance with C++11.<br />
** Remove <code>Slicer_ITKV3_COMPATIBILITY</code> build option.<br />
** Add option <code>Slicer_USE_ITKPython</code> to turn on ITK Python wrapping.<br />
** Removed duplicated code using ITK version of MGHIO.<br />
<br />
* Python<br />
** Added support writing scripted modules and widgets as new-style Python classes. <br />
** Simplify scripted module introducing SlicerPythonCppAPI. <br />
** Introduced qSlicerScriptedUtils::executeFile() <br />
** Updated CTK to include new PythonQt C++/Python ownership tracking feature. <br />
** Import scripted module as python module to avoid module top-level variables to clobber each other. [http://www.na-mic.org/Bug/view.php?id=3549 #3549]<br />
<br />
* Platform support<br />
** Fix support for 32-bit build allowing use of Slicer on Surface tablet.<br />
<br />
* Packaging & Testing infrastructure<br />
** Capturing VTK errors/warnings during testing.<br />
** Update extension build system to report packaging error on CDash.<br />
<br />
* Rendering / Visualization<br />
** Add Slicer_VTK_RENDERING_BACKEND configure option<br />
<br />
* MRML<br />
** Add support in vtkMRMLNode for multiple references to the same node. <br />
** Introducing InvokeCustomModifiedEvent. <br />
<br />
* ApplicationLogic<br />
** Added function PropagateLabelVolumeSelection(), PropagateForegroundVolumeSelection() and PropagateBackgroundVolumeSelection()<br />
<br />
* VolumeRenderingLogic<br />
** Extend volume rendering logic API adding GetPresetByName function. <br />
<br />
* View management<br />
** Add qMRMLLayoutViewFactory <br />
** Add utility method to display node in only 1 view <br />
<br />
<br />
<gallery caption="Improved Toolkits" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:CTK-Logo.png|Moved from CTK [https://github.com/commontk/CTK/commit/f64b68a f64b68a] to [https://github.com/commontk/CTK/commit/1c97e54 1c97e54] (499 commits) <!-- git log --oneline f64b68acd717dab060db41e8bee3f0f30df1a58f...1c97e5426f898bc7d074e6122992d0dd12bab56b --no-merges | wc -l --><br />
<br />
Image:CTKApplauncher_Logo.png|Moved from CTKAppLauncher v0.1.11 to v0.1.14 (43 commits) <!-- git log --oneline v0.1.11..v0.1.14 --no-merges | wc -l --><br />
<br />
Image:ITK_logo.png|Moved from ITK v4.4.1 to v4.6.0 (1089 commits) <!-- git log --oneline v4.4.1..56fae27 --no-merges | wc -l --><br />
<br />
Image:OpenIGTLink-Logo.png|Moved from OpenIGTLink [https://github.com/openigtlink/OpenIGTLink/compare/66e272d...849b434 66e272d to 849b434] (53 commits) <!-- git log --no-merges --oneline 66e272d..849b434 | wc -l --><br />
<br />
Image:Qt-logo.png |Moved from Qt 4.7.4 to Qt 4.8.6<br />
<br />
Image:VTK_logo.png|Moved from VTK v5.10.1 to VTK v6.2.0 (5490 commits) <!-- git log --oneline v5.10.1..b55dad7 --no-merges | wc -l --><br />
<br />
</gallery><br />
<br />
== Looking at the Code Changes ==<br />
<br />
From a git checkout you can easily see the all the commits since the time of the 4.4.0 release:<br />
<br />
git log v4.4.0..HEAD<br />
<br />
To see a summary of your own commits, you could use something like:<br />
<br />
git log v4.4.0..HEAD --oneline --author=me<br />
<br />
see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.<br />
<br />
[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]<br />
<br />
= Related Projects =<br />
<gallery caption="" widths="250px" heights="150px" perrow="3"><br />
</gallery></div>Nicolehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Announcements&diff=43199Documentation/Nightly/Announcements2015-11-02T16:03:35Z<p>Nicole: /* Slicer {{documentation/version}} Highlights */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
__NOTOC__<br />
<br />
<br />
<br />
{|width="100%"<br />
|align="center"|<br />
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]<br />
|}<br />
<br />
<br />
{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"<br />
|[[#Summary|Summary ]]<br />
|[[#What is 3D Slicer|What is 3D Slicer]]<br />
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]<br />
|[[#Slicer Training|Slicer Training]]<br />
|[[#Slicer Extensions|Slicer Extensions]]<br />
|[[#Other Improvements, Additions & Documentation|Other Improvements, Additions & Documentation]]<br />
|}<br />
<br />
= Summary = <br />
<br />
The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.<br />
<br />
* Slicer {{documentation/version}} introduces <br />
** An improved App Store, known as the Extension Manager, for adding plug-ins to Slicer. More than 80 plug-ins and packages of plug-ins are currently available.<br />
** Close to 150 feature improvements and bug fixes have resulted in improved performance and stability.<br />
** Improvements to many modules.<br />
<br />
* Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and the bug tracker. <br />
* Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer are not fully tested.<br />
* The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of tutorials and data sets for training in the use of Slicer. <br />
<br />
[http://www.slicer.org slicer.org] is the portal to the application, training materials, and the development community.<br />
<br />
= What is 3D Slicer =<br />
{{:Documentation/{{documentation/version}}/Slicer}}<br />
<br />
= Slicer {{documentation/version}} Highlights =<br />
<br />
<gallery caption="New and Improved Modules" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:Grid3dVolume.png|Improved [[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] module with support for non-linear transforms, visualization of transforms in 2D and 3D, detailed transform properties view - '''[https://www.youtube.com/watch?v=kZUAfR0mqqI click here for demo video]'''.<ul><li>Added support for copy/paste of linear transforms</li><li>Support saving of any transform to a grid transform</li><li> Improved composite transform support</li><li>Added support for thin plate spline transforms</li><li>Addressed display issue for slice intersection display of non-linearly transformed model</li></ul><br />
<br />
Image:DICOM Screenshot.png |The user interface of the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module has been improved for a better usability.<ul><li>Improved DICOM browser adding a right click menu to allow deleting or exporting to disk at the patients/studies/series levels.</li><li>Added support for DICOM private dictionary.</li><li>Improved support for loading of DICOM referenced datasets.</li><li>Read and apply window/level found in DICOM volumes.</li><li>Added support for Philips DWI datasets</li><li>Fixed loading of DICOM image from files containing special characters.</li></ul><br />
<br />
Image:20141116_SubjectHierarchyAnnouncement.png|Improved [[Documentation/Nightly/Modules/SubjectHierarchy|Subject hierarchy]] module for organizing and manipulating data loaded in Slicer.<ul><li>Highlight nodes in subject hierarchy referenced by DICOM</li><li>Added Transforms subject hierarchy plugin</li><li>Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]]. [http://www.na-mic.org/Bug/view.php?id=3163 #3163]</li><li>Added generic folder plugin to subject hierarchy</li><li>Subject hierarchy nodes automatically created for supported types</li><li>Added auto-delete subject hierarchy children to Application Settings </li><li>Added auto-create subject hierarchy option to Application Settings </li><li>Subject hierarchy tree headers show icons instead of text </li><li>Fixed subject hierarchy nodes creation when importing old scene [http://www.na-mic.org/Bug/view.php?id=3902 #3902]</li><li>Fixed volume visibility controls. [http://www.na-mic.org/Bug/view.php?id=3893 #3893]</li></ul><br />
<br />
<br />
</gallery><br />
<br />
= Slicer Training =<br />
<br />
The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of updated tutorials and data sets for training in the use of Slicer {{documentation/version}}. <br />
<br />
<br />
<gallery caption="New Tutorials" widths="250px" heights="150px" perrow="4"><br />
<br />
Image:2014-Slicer-Iowa-crop.png|This is an example of description {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
<br />
</gallery><br />
<br />
=Slicer Extensions=<br />
<br />
<gallery caption="New Extensions" widths="250px" heights="150px" perrow="4"><br />
<br />
Image:AnglePlanes Logo.png|[[Documentation/{{documentation/version}}/Extensions/AnglePlanes|AnglePlanes]] This Module is used to calculate the angle between two planes by using the normals {{new}}<br />
<br />
Image:Chest_Imaging_Platform.png|[http://www.chestimagingplatform.org/ Chest_Imaging_Platform] Chest Imaging Platform is an extension for quantitative CT imaging biomarkers for lung diseases {{new}}<br />
<br />
Image:DebuggingTools.png|[[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]] This extension contains various tools useful for developing and debugging modules {{new}}<br />
<br />
Image:SlicerExtension-DeveloperToolsForExtensions.png|[[Documentation/{{documentation/version}}/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] This extension offers different tools to help developers when they create Slicer extension {{new}}<br />
<br />
Image:DTI-Reg.png|[[Documentation/{{documentation/version}}/Extensions/DTI-Reg|DTI-Reg]] DTI-Reg is an extension that performs pair-wise DTI registration, using scalar FA map to drive the registration {{new}}<br />
<br />
Image:EasyClipLogo.png|[[Documentation/{{documentation/version}}/Extensions/EasyClip|EasyClip]] This Module is used to clip one or different 3D Models according to a predetermined plane {{new}}<br />
<br />
Image:GraphCutSegment.png|[http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html GraphCutSegment] This is a segment extension using graph cut and star shape algorithm {{new}}<br />
<br />
Image:LumpNav.png|[https://github.com/SlicerIGT/LumpNav LumpNav] Breast tumor resection using tracked ultrasound and cautery {{new}}<br />
<br />
Image:MarginCalculator Logo2 128.png|[[Documentation/{{documentation/version}}/Extensions/MarginCalculator|MarginCalculator]] The Matlab Bridge extension allows running Matlab scripts as command-line interface (CLI) modules directly from 3D Slicer {{new}}<br />
<br />
Image:MeshStatisticsExtension.png|[[Documentation/{{documentation/version}}/Extensions/MeshStatistics|MeshStatistics]] Mesh Statistics allows users to compute descriptive statistics over specific and predefined regions {{new}}<br />
<br />
Image:Icon1.png|[[Documentation/{{documentation/version}}/Extensions/MeshToLabelMap|MeshToLabelMap]] This extension computes a label map from a 3D model {{new}}<br />
<br />
Image:PET-IndiC.png|[[Documentation/{{documentation/version}}/Extensions/PET-IndiC|PET-IndiC]] The PET-IndiC Extension allows for fast segmentation of regions of interest and calculation of quantitative indices {{new}}<br />
<br />
Image:DPetBrainQuantification.png|[http://gti-fing.github.io/SlicerPetSpectAnalysis/ PetSpectAnalysis] First Version of the Pet Spect Analysis Extension {{new}}<br />
<br />
Image:PETTumorSegmentationExtensionIcon.png|[[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PETTumorSegmentation]] Tumor and lymph node segmentation in PET scans {{new}}<br />
<br />
Image:PickAndPaintExtension.png|[[Documentation/{{documentation/version}}/Extensions/PickAndPaint|PickAndPaint]] Pick 'n Paint tool allows users to select ROIs on a reference model and to propagate it over different time point models {{new}}<br />
<br />
Image:Q3DC.png|[[Documentation/{{documentation/version}}/Extensions/Q3DC|Q3DC]] This extension contains one module of the same name {{new}}<br />
<br />
Image:ResampleDTIlogEuclidean-128x128-icon.png|[[Documentation/{{documentation/version}}/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] This resamples Diffusion Tensor Images (DTI) in the log-euclidean framework {{new}}<br />
<br />
Image:SlicerHeart Logo 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerHeart|SlicerHeart]] Modules for cardiac analysis and intervention planning and guidance {{new}}<br />
<br />
Image:SlicerProstate Logo 1.0 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerProstate|SlicerProstate]] SlicerProstate extension hosts various modules to facilitate processing and management of prostate image data, utilizing prostate images in image-guided interventions and development of the imaging biomarkers of the prostate cancer {{new}}<br />
<br />
Image:Slicer-Wasp.png|[https://github.com/Tomnl/Slicer-Wasp Slicer-Wasp] A module to perform a series of ITK watershed segmentation (without seeds) and then let the user create a label map out of selected components {{new}}<br />
<br />
Image:T1 Mapping Logo Resized.png|[[Documentation/{{documentation/version}}/Extensions/T1Mapping|T1Mapping]] T1 mapping estimates effective tissue parameter maps (T1) from multi-spectral FLASH MRI scans with different flip angles {{new}}<br />
<br />
<!-- You could user either {{new}} or {{updated}} macros. --><br />
</gallery><br />
<br />
== Improved Extensions in Slicer 4.5 ==<br />
<br />
* [http://www.nitrc.org/projects/abc ABC]<br />
* [[Documentation/{{documentation/version}}/Extensions/CMFreg|CMFreg]]<br />
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]]<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]]<br />
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetryAnalysis]]<br />
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]]<br />
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|MatlabBridge]]<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]]<br />
* [[Documentation/{{documentation/version}}/Extensions/NeedleFinder|NeedleFinder]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PETDICOMExtension]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]<br />
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]]<br />
* [[Documentation/{{documentation/version}}/Extensions/VolumeClip|VolumeClip]]<br />
<br />
== Extensions removed from Slicer 4.5 ==<br />
<br />
* houghTransformCLI: Removed by the original author because it was not needed anymore.<br />
<br />
== Extensions renamed ==<br />
<br />
* PyDevRemoteDebug -> [[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]]<br />
* MultidimData -> [[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]]<br />
* TrackerStabilizer -> [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Slicer-TrackerStabilizer]]<br />
* AirwaySegmentation -> [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Slicer-AirwaySegmentation]]<br />
<br />
= Other Improvements, Additions & Documentation =<br />
<br />
== Optimization ==<br />
* Added support for loading of large images on windows. <br />
* Reduced the memory footprint by fixing memory leaks<br />
* Sped up by 2x slice rendering when the volume is linearly transformed. <br />
* Improved reslicing speed of quasi-axis-aligned slices. <br />
* Sped up annotation ROI display about 10x faster (100ms to 10ms). <br />
* Improved tractography display performance. <br />
* Prevent viewers flickering when only few nodes are removed.<br />
* Improved performance of transform widget.<br />
<br />
== Transforms ==<br />
* Added support for copy/paste of linear transforms.<br />
* Support saving of any transform to a grid transform. <br />
* Addressed translation slider instability in rotate first mode. <br />
* Improved composite transform support. <br />
* Added support for thin plate spline transforms. <br />
* Changed default ITK bspline transform writing file format to ITKv4. <br />
* Addressed display issue for slice intersection display of non-linearly transformed model. <br />
* Made transforms module translate-rotate first icon nicer.<br />
<br />
== DICOM ==<br />
* Improved DICOM browser allowing exporting to disk patients/studies/series using right click<br />
* Improved support for loading of DICOM referenced datasets.<br />
* Added support for DICOM private dictionary<br />
* Read and apply window/level found in DICOM volumes.<br />
* Added support for Philips DWI datasets<br />
* Fixed loading of DICOM image from files containing special characters.<br />
<br />
== Data processing ==<br />
* Added support for saving and loading of complex processing chain of CLI modules [http://www.na-mic.org/Bug/view.php?id=3240 #3240] [http://www.na-mic.org/Bug/view.php?id=3468 #3468]<br />
<br />
== CLI ==<br />
* Added support for transfer of fiducial file to/from CLI modules. <br />
* Added support for transfer of Hierarchy sub-scene to/from CLI modules. <br />
* Fixed loading multivolumes produced by CLI modules. <br />
<br />
== Usability ==<br />
* Built-in module categories and extensions categories are listed separately in module selector.<br />
* Allow multi-selection in subject hierarchy.<br />
* Generate high-resolution magnified screenshots for 3D view.<br />
<br />
== SubjectHierarchy ==<br />
* Highlight nodes in subject hierarchy referenced by DICOM <br />
* Added Transforms subject hierarchy plugin <br />
* Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]]. [http://www.na-mic.org/Bug/view.php?id=3163 #3163]<br />
* Added generic folder plugin to subject hierarchy <br />
* Subject hierarchy nodes automatically created for supported types <br />
* Added auto-delete subject hierarchy children to Application Settings <br />
* Added auto-create subject hierarchy option to Application Settings <br />
* Subject hierarchy tree headers show icons instead of text <br />
* Fixed subject hierarchy nodes creation when importing old scene [http://www.na-mic.org/Bug/view.php?id=3902 #3902]<br />
* Fixed volume visibility controls. [http://www.na-mic.org/Bug/view.php?id=3893 #3893]<br />
<br />
== Python scripting ==<br />
* Upgraded from Numpy 1.4.1 to NumPy 1.9.2<br />
* Upgraded from Python 2.7.3 to Python 2.7.10<br />
* Bundled nose python module into the Slicer package.<br />
* Added logging functions for Python. <br />
* Fixed VTKObservationMixin and added [[Documentation/Nightly/Developers/Python_scripting#How_can_I_access_callData_argument_in_a_VTK_object_observer_callback_function|documentation]].<br />
* Updated IOManager and DICOMWidgets to emit <code>newFileLoaded()</code>.<br />
* Added logging of Python console user input.<br />
* Added accessor for vertex points of models as numpy array. <br />
* Allow displayable manager to be introspected using python. <br />
<br />
== Editor ==<br />
* Warn user when GrowCut effect is attempted with unsupported image type. <br />
* Added ability to delete only the selected structure. <br />
* Ensure label map is updated each time a master volume is selected. <br />
* Improved threshold paint effect to have inclusive ranges [http://www.na-mic.org/Bug/view.php?id=4066 #4066]<br />
* Remember pain radius when effect are changed [http://www.na-mic.org/Bug/view.php?id=1853 #1853]<br />
* Reset editor interface when scene is closed. <br />
* Ensure a related merge volume is selected after a structure deleted. <br />
<br />
== Markups ==<br />
* Added ability to refocus 3d cameras on a fiducial. [http://www.na-mic.org/Bug/view.php?id=3683 #3683]<br />
<br />
== LabelMapVolumeNode ==<br />
* TBD<br />
* Added labelmap node support to subject hierarchy <br />
* Improved CLI image widget type handling. <br />
<br />
== Slice viewers ==<br />
* Added control to adjust thickness for label map outlines [http://www.na-mic.org/Bug/view.php?id=2267 #2267]<br />
<br />
== DataProbe ==<br />
* Added magnified slice view into DataProbe panel. <br />
<br />
== SliceViewAnnotations ==<br />
* Added orientation marker to slice view annotations. <br />
* Improved integration of SliceViewAnnotations. [http://www.na-mic.org/Bug/view.php?id=3943 #3943]<br />
<br />
== OpenIGTLink ==<br />
* Improved support for POINT and POLYDATA messages. [http://www.na-mic.org/Bug/view.php?id=3875 #3875] [http://www.na-mic.org/Bug/view.php?id=3907 #3907]<br />
<br />
== DoubleArrays ==<br />
* Improved loading and saving of measurement files (.mcsv) <br />
<br />
== CastScalarVolume ==<br />
* Improved CastScalarVolume module to support input of type unsigned char, int or long. <br />
<br />
== SceneView ==<br />
* Improved management of data loaded between creation of SceneViews<br />
<br />
== Landmark ==<br />
* Added support for landmark refinement <br />
* Improved LandmarkRegistration plugin loader displaying message if plugin failed to be loaded.<br />
<br />
== MultiVolumeImporter ==<br />
* Fixed loading of MGH variable FA multivolume. <br />
<br />
== FiberBundleLabelSelect ==<br />
* Fixed ADD operation for ‘Label to include’. [http://www.na-mic.org/Bug/view.php?id=4025 #4025]<br />
* Added support for both VTK and VTP input files.<br />
<br />
== DTI support ==<br />
* Resolved multithread issue that caused errors with multiple b values. [http://www.na-mic.org/Bug/view.php?id=3977 #3977]<br />
* Fixed parallel/perpendicular diffusivity on glyphs, interactive seeding line display. [http://www.na-mic.org/Bug/view.php?id=3857 #3857]<br />
* Fixed displaying of Tensor properties and their ranges in Tractography display module for lines/tubes/glyphs [http://www.na-mic.org/Bug/view.php?id=3857 #3857]<br />
* Added logic for propagating color and opacity to fiber hierarchies. [http://www.na-mic.org/Bug/view.php?id=3925 #3925]<br />
* Added support for Fiber Hierarchies in the Models Module. [http://www.na-mic.org/Bug/view.php?id=3678 #3678]<br />
<br />
== VolumeRendering ==<br />
* Fixed volume rendering not visible when non-volume-rendered volume is frequently changing in the scene. <br />
* Ensure volume rendering is updated when volume geometry is modified. [http://www.na-mic.org/Bug/view.php?id=4023 #4023]<br />
<br />
== FiberTractMeasurements ==<br />
* TBD<br />
* Added CLI module FiberTractMeasurements allowing to XXXX supporting cluster aggregation.<br />
<br />
= For Developers =<br />
<br />
== Modules and Extensions ==<br />
<br />
* ExtensionWizard<br />
** Added "Enable developer mode" option to ExtensionWizard<br />
<br />
* SelfTests<br />
** Allow self tests to set a custom delay for message display<br />
<br />
* MRMLNodeComboBox<br />
** Allow qMRMLNodeComboBox base name setting for each node type <br />
** Added removeAttribute function to MRML node comboboxes and proxy model <br />
** Multiple node types can be created in qMRMLNodeComboBox <br />
** Support custom behavior for default actions. <br />
<br />
* MRML Scene introspection<br />
** Added node printself output to node inspector <br />
<br />
* Message logging<br />
** Added vtkInfoMacro<br />
<br />
* DICOM<br />
** Package additional DCMTK applications: echoscu, dsr2html, xml2dcm and xml2dsr<br />
<br />
* Markups<br />
** Signal end fiducial interaction in 3D <br />
** Add reusable simple markups widget <br />
<br />
* Module API<br />
** Extend module API with "widgetRepresentationCreationEnabled" property<br />
<br />
* Slicerlets<br />
** Allow slicelets and Slicer tests to handle log messages. <br />
<br />
* Units<br />
** Added extra units support: frequency, velocity and intensity.<br />
** Extended Units logic API adding GetDisplayCoefficient() and GetSIPrefixCoefficient() <br />
** Updated MRMLUnitNode to ensure value to string conversion account for precision. <br />
<br />
* SubjectHierarchy<br />
** Introduced adaptor classes facilitating implementation of python scripted subject hierarchy plugins. <br />
** Introduced autoDeleteSubjectHierarchyChildren property <br />
<br />
* Editor<br />
** Facilitate re-use of Editor python components in extension (LabelStructureListWidget in 043f398)<br />
** Updated EditUtil API adding function SetUseLabelOutline() to explicitly set label outline state on all Slice nodes<br />
<br />
== Slicer Core ==<br />
<br />
* IDE integration<br />
** Improve build targets organization in IDE that support folders.<br />
** VisualStudio: Do not build documentation when F7 is pressed.<br />
** Facilitate integration with python IDE allowing minimal 'slicer' module to be imported.<br />
<br />
* Build-system<br />
** Add support for Visual Studio 2013.<br />
** Update build system anticipating transition to modern CMake.<br />
** Update MacOSX packaging infrastructure anticipating the signing of package in future release.<br />
** Update code base anticipitating compliance with C++11.<br />
** Remove <code>Slicer_ITKV3_COMPATIBILITY</code> build option.<br />
** Add option <code>Slicer_USE_ITKPython</code> to turn on ITK Python wrapping.<br />
** Removed duplicated code using ITK version of MGHIO.<br />
<br />
* Python<br />
** Added support writing scripted modules and widgets as new-style Python classes. <br />
** Simplify scripted module introducing SlicerPythonCppAPI. <br />
** Introduced qSlicerScriptedUtils::executeFile() <br />
** Updated CTK to include new PythonQt C++/Python ownership tracking feature. <br />
** Import scripted module as python module to avoid module top-level variables to clobber each other. [http://www.na-mic.org/Bug/view.php?id=3549 #3549]<br />
<br />
* Platform support<br />
** Fix support for 32-bit build allowing use of Slicer on Surface tablet.<br />
<br />
* Packaging & Testing infrastructure<br />
** Capturing VTK errors/warnings during testing.<br />
** Update extension build system to report packaging error on CDash.<br />
<br />
* Rendering / Visualization<br />
** Add Slicer_VTK_RENDERING_BACKEND configure option<br />
<br />
* MRML<br />
** Add support in vtkMRMLNode for multiple references to the same node. <br />
** Introducing InvokeCustomModifiedEvent. <br />
<br />
* ApplicationLogic<br />
** Added function PropagateLabelVolumeSelection(), PropagateForegroundVolumeSelection() and PropagateBackgroundVolumeSelection()<br />
<br />
* VolumeRenderingLogic<br />
** Extend volume rendering logic API adding GetPresetByName function. <br />
<br />
* View management<br />
** Add qMRMLLayoutViewFactory <br />
** Add utility method to display node in only 1 view <br />
<br />
<br />
<gallery caption="Improved Toolkits" widths="350px" heights="250px" perrow="3"><br />
<br />
Image:CTK-Logo.png|Moved from CTK [https://github.com/commontk/CTK/commit/f64b68a f64b68a] to [https://github.com/commontk/CTK/commit/1c97e54 1c97e54] (499 commits) <!-- git log --oneline f64b68acd717dab060db41e8bee3f0f30df1a58f...1c97e5426f898bc7d074e6122992d0dd12bab56b --no-merges | wc -l --><br />
<br />
Image:CTKApplauncher_Logo.png|Moved from CTKAppLauncher v0.1.11 to v0.1.14 (43 commits) <!-- git log --oneline v0.1.11..v0.1.14 --no-merges | wc -l --><br />
<br />
Image:ITK_logo.png|Moved from ITK v4.4.1 to v4.6.0 (1089 commits) <!-- git log --oneline v4.4.1..56fae27 --no-merges | wc -l --><br />
<br />
Image:OpenIGTLink-Logo.png|Moved from OpenIGTLink [https://github.com/openigtlink/OpenIGTLink/compare/66e272d...849b434 66e272d to 849b434] (53 commits) <!-- git log --no-merges --oneline 66e272d..849b434 | wc -l --><br />
<br />
Image:Qt-logo.png |Moved from Qt 4.7.4 to Qt 4.8.6<br />
<br />
Image:VTK_logo.png|Moved from VTK v5.10.1 to VTK v6.2.0 (5490 commits) <!-- git log --oneline v5.10.1..b55dad7 --no-merges | wc -l --><br />
<br />
</gallery><br />
<br />
== Looking at the Code Changes ==<br />
<br />
From a git checkout you can easily see the all the commits since the time of the 4.4.0 release:<br />
<br />
git log v4.4.0..HEAD<br />
<br />
To see a summary of your own commits, you could use something like:<br />
<br />
git log v4.4.0..HEAD --oneline --author=me<br />
<br />
see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.<br />
<br />
[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]<br />
<br />
= Related Projects =<br />
<gallery caption="" widths="250px" heights="150px" perrow="3"><br />
</gallery></div>Nicolehttps://www.slicer.org/w/index.php?title=File:Slicer-Editor-Terminology-0.tif&diff=43048File:Slicer-Editor-Terminology-0.tif2015-10-20T18:45:02Z<p>Nicole: </p>
<hr />
<div></div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings/20151020&diff=43002Developer Meetings/201510202015-10-15T20:37:17Z<p>Nicole: Created page with '= Update = = To Discuss= * Nicole: Adding terminology information to Editor, [https://github.com/fedorov/Reporting/issues/52 Reporting issue #52] = Conclusion = Attendees: D…'</p>
<hr />
<div>= Update =<br />
<br />
= To Discuss=<br />
* Nicole: Adding terminology information to Editor, [https://github.com/fedorov/Reporting/issues/52 Reporting issue #52]<br />
<br />
<br />
= Conclusion =<br />
Attendees: <br />
<br />
Discussion of agenda items:</div>Nicolehttps://www.slicer.org/w/index.php?title=Developer_Meetings&diff=43001Developer Meetings2015-10-15T20:35:51Z<p>Nicole: /* 2015 */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!--<br />
<center>[[File:ScreenShot_GoogleHangout.PNG|300px]]</center><br />
--><br />
<br />
== Introduction ==<br />
The Slicer engineering team is distributed across several locations. Because of this, we use a variety of electronic means for communication. In addition to the twice a year [http://wiki.na-mic.org/Wiki/index.php/Project_Events project weeks], and additional topic oriented meeting, we have a weekly Google hangout meeting every Tuesday @ 2pm EST. <br />
<br />
These meetings are open to anyone. If you are interested, please join the [https://plus.google.com/u/1/communities/105715968666294296532 3DSlicer BarCamp] community on Google Plus.<br />
<br />
<br><br />
{{mbox<br />
| type = style<br />
| text = <big>Open to everyone - Every Tuesday @ 2pm EST on [https://plus.google.com/u/0/communities/105715968666294296532/events 3DSlicer BarCamp] community</big><br />
| image= [[File:smile.png|40px]]<br />
}}<br />
<br><br />
<br />
<br />
<small>[[Developer_Meetings/OrganizerInstruction|How to schedule a hangout ?]]</small><br />
<br><small>[[Documentation/Nightly/FAQ/BarCamp#Moderators:_How_to_approve.2Freject_requests_.3F|Moderators:How to approve/reject requests?]]</small><br />
<br />
== 2015 ==<br />
* [[Developer_Meetings/20151020|October 20th, 2015]]<br />
* [[Developer_Meetings/20151013|October 13th, 2015]]<br />
* [[Developer_Meetings/20151006|October 6th, 2015]]<br />
* [[Developer_Meetings/20150929|September 29th, 2015]]<br />
* [[Developer_Meetings/20150922|September 22nd, 2015]]<br />
* [[Developer_Meetings/20150915|September 15th, 2015]]<br />
* [[Developer_Meetings/20150908|September 8th, 2015]]<br />
* [[Developer_Meetings/20150901|September 1st, 2015]]<br />
* [[Developer_Meetings/20150825|August 25th, 2015]]<br />
* [[Developer_Meetings/20150818|August 18th, 2015]]<br />
* [[Developer_Meetings/20150811|August 11th, 2015]]<br />
* [[Developer_Meetings/20150804|August 4th, 2015]]<br />
* [[Developer_Meetings/20150728|July 28th, 2015]]<br />
* [[Developer_Meetings/20150714|July 14th, 2015]]<br />
* [[Developer_Meetings/20150707|July 7th, 2015]]<br />
* June 23rd, 2015 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2015_Summer_Project_Week Summer project week]</small><br />
* [[Developer_Meetings/20150616|June 16th, 2015]]<br />
* [[Developer_Meetings/20150609|June 9th, 2015]]<br />
* [[Developer_Meetings/20150602|June 2nd, 2015]]<br />
* [[Developer_Meetings/20150526|May 26th, 2015]]<br />
* [[Developer_Meetings/20150519|May 19th, 2015]]<br />
* [[Developer_Meetings/20150512|May 12th, 2015]]<br />
* [[Developer_Meetings/20150505|May 5th, 2015]]<br />
* [[Developer_Meetings/20150428|April 28st, 2015]]<br />
* [[Developer_Meetings/20150421|April 21st, 2015]]<br />
* [[Developer_Meetings/20150414|April 14th, 2015]]<br />
* [[Developer_Meetings/20150407|April 7th, 2015]]<br />
* [[Developer_Meetings/20150331|March 31st, 2015]]<br />
* [[Developer_Meetings/20150324|March 24th, 2015]]<br />
* [[Developer_Meetings/20150317|March 17th, 2015]]<br />
* [[Developer_Meetings/20150310|March 10th, 2015]]<br />
* [[Developer_Meetings/20150303|March 3rd, 2015]]<br />
* [[Developer_Meetings/20150224|February 24th, 2015]]<br />
* [[Developer_Meetings/20150224|February 24th, 2015]]<br />
* [[Developer_Meetings/20150217|February 17th, 2015]]<br />
* [[Developer_Meetings/20150210|February 10th, 2015]]<br />
* [[Developer_Meetings/20150203|February 3rd, 2015]]<br />
* [[Developer_Meetings/20150127|January 27th, 2015]]<br />
* [[Developer_Meetings/20150120|January 20th, 2015]]<br />
* [[Developer_Meetings/20150113|January 13th, 2015]]<br />
* January 6th, 2015 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Winter project week]</small><br />
<br />
== 2014 ==<br />
* [[Developer_Meetings/20141230|December 30th, 2014]]<br />
* [[Developer_Meetings/20141223|December 23rd, 2014]]<br />
* [[Developer_Meetings/20141216|December 16th, 2014]]<br />
* [[Developer_Meetings/20141209|December 9th, 2014]]<br />
* [[Developer_Meetings/20141202|December 2nd, 2014]]<br />
* [[Developer_Meetings/20141125|November 25th, 2014]]<br />
* [[Developer_Meetings/20141118|November 18th, 2014]]<br />
* [[Developer_Meetings/20141111|November 11th, 2014]]<br />
* [[Developer_Meetings/20141103|November 3rd, 2014]]<br />
* [[Developer_Meetings/20141029|October 29th, 2014]]<br />
* [[Developer_Meetings/20141021|October 21st, 2014]]<br />
* [[Developer_Meetings/20141014|October 14th, 2014]]<br />
* [[Developer_Meetings/20141007|October 7th, 2014]]<br />
* [[Developer_Meetings/20140930|September 30th, 2014]]<br />
* [[Developer_Meetings/20140923|September 23rd, 2014]]<br />
* [[Developer_Meetings/20140916|September 16th, 2014]]<br />
* [[Developer_Meetings/20140909|September 9th, 2014]]<br />
* [[Developer_Meetings/20140901|September 1st, 2014]]<br />
* [[Developer_Meetings/20140826|August 26th, 2014]]<br />
* [[Developer_Meetings/20140819|August 19th, 2014]]<br />
* [[Developer_Meetings/20140812|August 12th, 2014]]<br />
* [[Developer_Meetings/20140805|August 5th, 2014]]<br />
* [[Developer_Meetings/20140729|July 29th, 2014]]<br />
* [[Developer_Meetings/20140722|July 22nd, 2014]]<br />
* [[Developer_Meetings/20140715-2|July 15th, 2014]] <small>Developer hangout</small><br />
* [[Developer_Meetings/20140715|July 15th, 2014]] <small>Extension Developers - From VTK5 to VTK6 - Q&A- Google Hangout</small><br />
* [[Developer_Meetings/20140701|July 1st, 2014]]<br />
* June 24th, 2014 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/2014_Summer_Project_Week 19th NA-MIC project week]</small><br />
* [[Developer_Meetings/20140617|June 17th, 2014]]<br />
* [[Developer_Meetings/20140610|June 10th, 2014]]<br />
* [[Developer_Meetings/20140603|June 3rd, 2014]]<br />
* [[Developer_Meetings/20140527|May 27th, 2014]]<br />
* [[Developer_Meetings/20140520|May 20th, 2014]]<br />
* [[Developer_Meetings/20140513|May 13th, 2014]]<br />
* May 6th, 2014 - <small>Cancelled - [http://www.commontk.org/index.php/CTK-Hackfest-May-2014 CTK Hackfest in St Louis]</small><br />
* [[Developer_Meetings/20140429|April 29th, 2014]]<br />
* [[Developer_Meetings/20140422|April 22th, 2014]]<br />
* [[Developer_Meetings/20140415|April 15th, 2014]]<br />
* [[Developer_Meetings/20140408|April 8th, 2014]]<br />
* [[Developer_Meetings/20140401|April 1st, 2014]]<br />
* [[Developer_Meetings/20140325|March 25th, 2014]]<br />
* [[Developer_Meetings/20140318|March 18th, 2014]]<br />
* [[Developer_Meetings/20140311|March 11th, 2014]]<br />
* [[Developer_Meetings/2014030607|March 6-7, 2014 (Face to Face in Boston)]]<br />
* [[Developer_Meetings/20140304|March 4th, 2014]]<br />
* [[Developer_Meetings/20140225|February 25th, 2014]]<br />
* [[Developer_Meetings/20140218|February 18th, 2014]]<br />
* [[Developer_Meetings/20140211|February 11th, 2014]]<br />
* [[Developer_Meetings/20140204|February 4th, 2014]]<br />
* [[Developer_Meetings/20140128|January 28th, 2014]]<br />
* [[Developer_Meetings/20140121|January 21st, 2014]]<br />
* [[Developer_Meetings/20140114|January 14th, 2014]]<br />
* January 7th, 2014 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/AHM_2014 AHM in Salt Lake City]</small><br />
<br />
== 2013 ==<br />
* December 31th, 2013 - <small>Cancelled - New year day</small><br />
* December 24th, 2013 - <small>Cancelled - Christmas day</small><br />
* [[Developer_Meetings/20131217|December 17, 2013]]<br />
* [[Developer_Meetings/20131210|December 10, 2013]]<br />
* [[Developer_Meetings/20131203|December 3rd, 2013]]<br />
* [[Developer_Meetings/20131126|November 26th, 2013]]<br />
* [[Developer_Meetings/20131119|November 19th, 2013]]<br />
* [[Developer_Meetings/20131112|November 12th, 2013]]<br />
* [[Developer_Meetings/20131105|November 5th, 2013]]<br />
* [[Developer_Meetings/20131029|October 29th, 2013]]<br />
* [[Developer_Meetings/20131022|October 22th, 2013]]<br />
* [[Developer_Meetings/20131015|October 15th, 2013]]<br />
* [[Developer_Meetings/20131008|October 8th, 2013]]<br />
* [[Developer_Meetings/20131001|October 1st, 2013]]<br />
* [[Developer_Meetings/20130924|September 24th, 2013]]<br />
* [[Developer_Meetings/20130917|September 17th, 2013]]<br />
* [[Developer_Meetings/20130910|September 10th, 2013]]<br />
* [[Developer_Meetings/20130903|September 3rd, 2013]]<br />
* [[Developer_Meetings/20130827|August 27th, 2013]]<br />
* [[Developer_Meetings/20130820|August 20th, 2013]]<br />
* [[Developer_Meetings/20130813|August 13th, 2013]]<br />
* [[Developer_Meetings/20130806|August 6th, 2013]]<br />
* [[Developer_Meetings/20130730|July 30th, 2013]]<br />
* [[Developer_Meetings/20130723|July 23rd, 2013]]<br />
* [[Developer_Meetings/20130716|July 16th, 2013]]<br />
* [[Developer_Meetings/20130709|July 9th, 2013]]<br />
* [[Developer_Meetings/20130702|July 2nd, 2013]]<br />
* June 18th, 23rd 2013 - cancelled due to NA-MIC Project week<br />
* [[Developer_Meetings/20130611|June 11th, 2013]]<br />
* [[Developer_Meetings/20130604|June 4th, 2013]]<br />
* [[Developer_Meetings/20130528|May 28th, 2013]]<br />
* May 21th, 2013 - <small>Cancelled - [http://www.commontk.org/index.php/CTK-Hackfest-May-2013 CTK Hackfest in Canada]</small><br />
* [[Developer_Meetings/20130514|May 14th, 2013]]<br />
* [[Developer_Meetings/20130507|May 7th, 2013]]<br />
* [[Developer_Meetings/20130430|April 30th, 2013]]<br />
* [[Developer_Meetings/20130423|April 23th, 2013]]<br />
* [[Developer_Meetings/20130416|April 16th, 2013]]<br />
* [[Developer_Meetings/20130409|April 9th, 2013]]<br />
* [[Developer_Meetings/20130402|April 2nd, 2013]]<br />
* [[Developer_Meetings/20130326|March 26th, 2013]]<br />
* [[Developer_Meetings/20130319|March 19th, 2013]]<br />
* [[Developer_Meetings/20130312|March 12th, 2013]]<br />
* [[Developer_Meetings/20130305|March 05th, 2013]]<br />
* [[Developer_Meetings/20130226|February 26th, 2013]]<br />
* [[Developer_Meetings/20130219|February 19th, 2013]]<br />
* [[Developer_Meetings/20130212|February 12th, 2013]]<br />
* [[Developer_Meetings/20130205|February 5th, 2013]]<br />
* [[Developer_Meetings/20130129|January 29th, 2013]]<br />
* [[Developer_Meetings/20130122|January 22nd, 2013]]<br />
* January 15th, 2013 - <small>Cancelled - AHM happened previous week</small><br />
* January 8th, 2013 - <small>Cancelled - [http://www.na-mic.org/Wiki/index.php/AHM_2013 AHM in Salt Lake City]</small><br />
* January 1st, 2013 - <small>Cancelled - New year day</small><br />
<br />
== 2012 ==<br />
* December 25th, 2012 - <small>Cancelled - Christmas day</small><br />
* [[Developer_Meetings/20121218|December 18th, 2012]]<br />
* [[Developer_Meetings/20121211|December 11th, 2012]]<br />
* [[Developer_Meetings/20121204|December 4th, 2012]]<br />
* [[Developer_Meetings/20121127|November 27th, 2012]]<br />
* [[Developer_Meetings/20121120|November 20th, 2012]]<br />
* [[Developer_Meetings/20121113|November 13th, 2012]]<br />
* [[Developer_Meetings/20121106|November 6th, 2012]]<br />
* [[Developer_Meetings/20121030|October 30th, 2012]]<br />
* [[Developer_Meetings/20121023|October 23th, 2012]]<br />
* [[Developer_Meetings/20121016|October 16th, 2012]]<br />
* [[Developer_Meetings/20121009|October 09th, 2012]]<br />
* [[Developer_Meetings/20121002|October 02th, 2012]]<br />
* [[Developer_Meetings/20120925|September 25th, 2012]]<br />
* [[Developer_Meetings/20120918|September 18th, 2012]]<br />
* [[Developer_Meetings/20120911|September 11th, 2012]]<br />
* [[Developer_Meetings/20120904|September 4th, 2012]]<br />
* [[Developer_Meetings/20120828|August 28th, 2012]]<br />
* [[Developer_Meetings/20120821|August 21st, 2012]]<br />
* [[Developer_Meetings/20120814|August 14th, 2012]]<br />
* [[Developer_Meetings/20120807|August 7th, 2012]]<br />
* [[Developer_Meetings/20120731|July 31th, 2012]]<br />
* [[Developer_Meetings/20120724|July 24th, 2012]]<br />
* [[Developer_Meetings/20120717|July 17th, 2012]]<br />
* [[Developer_Meetings/20120710|July 10th, 2012]]<br />
* [[Developer_Meetings/20120703|July 3rd, 2012]]<br />
* [[Developer_Meetings/20120626|June 26th, 2012]]<br />
* [[Developer_Meetings/20120619|June 19th, 2012]]<br />
* [[Developer_Meetings/20120612|June 12th, 2012]]<br />
* [[Developer_Meetings/20120605|June 5th, 2012]]<br />
* [[Developer_Meetings/20120529|May 29, 2012]]<br />
* [[Developer_Meetings/20120522|May 22, 2012]]<br />
* [[Developer_Meetings/20120515|May 15, 2012]]<br />
* [[Developer_Meetings/20120508|May 8, 2012]]<br />
* [[Developer_Meetings/20120501|May 1st, 2012]]<br />
<br />
=== Miscellaneous ===<br />
* [http://wiki.na-mic.org/Wiki/index.php/Slicer4.2Planning August 20st, 2012 - Slicer 4.2 planning]<br />
<br />
== 2010 - 2011 ==<br />
* See [[Slicer4:QtPort/MeetingNotes]]<br />
<br />
== 2009 ==<br />
* September 16-17: [[Slicer:Developer_Meetings:20090916|Slicer widgets brainstorming]] (rough notes)<br />
* February 3: [[Slicer:Developer_Meetings:20090203|mBIRN preparation, Slicer3.4 release]]<br />
<br />
== 2008 ==<br />
* September 16: Demian on Python/Tractography<br />
* August 26: [[Slicer:Developer_Meetings:20080826|Slicer and NA-MIC Overview]]<br />
* August 11: [http://www.na-mic.org/Wiki/index.php/Slicer3_Q%26A_2008-11-18 Introduction of new researchers and developers (17 attendees)]<br />
* July 29: [[Slicer:Developer_Meetings:20080729|Slicer 3.2 release]]<br />
<br />
== 2007 ==<br />
* July 16: [[Slicer:Developer_Meetings:20070716|PNL demo Slicer3]]<br />
* June 12: [[Slicer:Developer_Meetings:20070612|PNL wishlist for Slicer3]]<br />
* March 27: [[Slicer:Developer_Meetings:20070327|Slicer 2.7, Slicer3 beta]]<br />
* February 6: [[Slicer:Developer_Meetings:20070206|Slicer3 mBIRN meeting Prep]]<br />
* January 30: [[Slicer:Developer_Meetings:20070130|Slicer3 Release Planning]]<br />
* January 2: [[Slicer:Developer_Meetings:20070102|Slicer3 AHM Prep]]<br />
<br />
== 2006 ==<br />
* November 21: [[Slicer:Developer_Meetings:20061121|Slicer3 Updates, preparations for retreat]]<br />
* November 07: [[Slicer:Developer_Meetings:20061107|Slicer3 Updates, NA-MIC Mesh Kickoff]]<br />
* October 10: [[Slicer:Developer_Meetings:20061010| Slicer3 Updates]]<br />
* August 29: [[Slicer:Developer_Meetings:20060829|Slicer 3 and Slicer 2.6 bugs]]<br />
* May 2: [[Slicer:Developer_Meetings:20060502|Release 2.6, Fiducials, Slicer for MRT]]<br />
* March 14: [[Slicer:Developer_Meetings:20060314|Release 2.6, mBIRN meeting, Slicer MRT]]<br />
<br />
<br />
== 2005 ==<br />
* June 7: [[Slicer:Developer_Meetings:20050607|NA-MIC Programming Week discussion: Slicer 3]]<br />
* May 24: [[Slicer:Developer_Meetings:20050524|Release 2.5]]<br />
* May 10: [[Slicer:Developer_Meetings:20050510|Release 2.5]]<br />
* April 11: [[Slicer:Developer_Meetings:20050411|To-do list for release 2.5, OpenTracker]]<br />
* March 29: [[Slicer:Developer_Meetings:20050329|Dan Kacher : Integrating trackers with Slicer ]]<br />
* March 15: [[Slicer:Developer_Meetings:20050315|Updates from BIRN Meeting, Training, Windows Building, Release 2.5]]<br />
* March 1: [[Slicer:Developer_Meetings:20050301|Updates from NA-MIC Meeting, Current and Future Projects]]<br />
* February 1: [[Slicer:Developer_Meetings:20050201|Randy Ellis : demo of surgical navigation system]]<br />
* January 18: [[Slicer:Developer_Meetings:20050118|Slicer Architecture]]</div>Nicole