View source for Documentation/Nightly/Announcements

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{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Summary|Summary ]]
|[[#What is 3D Slicer|What is 3D Slicer]]
|[[#Slicer {{documentation/version}} Highlights|Slicer {{documentation/version}} Highlights]]
|[[#Slicer Training|Slicer Training]]
|[[#Slicer Extensions|Slicer Extensions]]
|[[#Other Improvements, Additions & Documentation|Other Improvements, Additions & Documentation]]
|}

= Summary = 

The [http://www.slicer.org/pages/Acknowledgments community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.

* Slicer {{documentation/version}} introduces 
** 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.
** Close to 150 feature improvements and bug fixes have resulted in improved performance and stability.
** Improvements to many modules.

* 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. 
* 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.
* The [[Documentation/{{documentation/version}}/Training|Slicer Training]] page provides a series of tutorials and data sets for training in the use of Slicer. 

[http://www.slicer.org slicer.org] is the portal to the application, training materials, and the development community.

= What is 3D Slicer =
{{:Documentation/{{documentation/version}}/Slicer}}

= Slicer {{documentation/version}} Highlights =

<gallery caption="New and Improved Modules" widths="350px" heights="250px" perrow="3">

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>

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>

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>


</gallery>

= Slicer Training =

* [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 [https://youtu.be/GGgP89uTOLo 3D Slicer Tutorial: How to Segment a Lumbar Vertebrae] has been added
* New dataset has been added to the [http://www.slicer.org/slicerWiki/images/1/1f/DiffusionMRIanalysis_Tutorial_SoniaPujol_2013.pdf 3D Slicer Diffusion Tensor Imaging Tutorial]
* New addition to the  [http://wiki.na-mic.org/Wiki/images/b/b2/DiffusionMRIanalysis_Tutorial_SoniaPujol_UNC2015.pdf DTI tutorial] with  brain masking section
* New [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Training#Slicer4_Image_Registration 3D Slicer Registration Tutorial] has been added to the compendium.
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}}. 


<gallery caption="New Tutorials" widths="250px" heights="150px" perrow="4">

Image:2014-Slicer-Iowa-crop.png|This is an example of description {{new}}

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</gallery>

=Slicer Extensions=

<gallery caption="New Extensions" widths="250px" heights="150px" perrow="4">

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}}

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}}

Image:DebuggingTools.png|[[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]] This extension contains various tools useful for developing and debugging modules {{new}}

Image:SlicerExtension-DeveloperToolsForExtensions.png|[[Documentation/{{documentation/version}}/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] This extension offers different tools to help developers when they create Slicer extension {{new}}

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}}

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}}

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}}

Image:LumpNav.png|[https://github.com/SlicerIGT/LumpNav LumpNav] Breast tumor resection using tracked ultrasound and cautery {{new}}

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}}

Image:MeshStatisticsExtension.png|[[Documentation/{{documentation/version}}/Extensions/MeshStatistics|MeshStatistics]] Mesh Statistics allows users to compute descriptive statistics over specific and predefined regions {{new}}

Image:Icon1.png|[[Documentation/{{documentation/version}}/Extensions/MeshToLabelMap|MeshToLabelMap]] This extension computes a label map from a 3D model {{new}}

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}}

Image:DPetBrainQuantification.png|[http://gti-fing.github.io/SlicerPetSpectAnalysis/ PetSpectAnalysis] First Version of the Pet Spect Analysis Extension {{new}}

Image:PETTumorSegmentationExtensionIcon.png|[[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PETTumorSegmentation]] Tumor and lymph node segmentation in PET scans with a specialized Editor effect {{new}}

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}}

Image:Q3DC.png|[[Documentation/{{documentation/version}}/Extensions/Q3DC|Q3DC]] This extension contains one module of the same name {{new}}

Image:ResampleDTIlogEuclidean-128x128-icon.png|[[Documentation/{{documentation/version}}/Extensions/ResampleDTIlogEuclidean|ResampleDTIlogEuclidean]] This resamples Diffusion Tensor Images (DTI) in the log-euclidean framework {{new}}

Image:SlicerHeart Logo 128x128.png|[[Documentation/{{documentation/version}}/Extensions/SlicerHeart|SlicerHeart]] Modules for cardiac analysis and intervention planning and guidance {{new}}

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}}

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}}

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}}

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</gallery>

== Improved Extensions in Slicer 4.5 ==

* [http://www.nitrc.org/projects/abc ABC]
* [[Documentation/{{documentation/version}}/Extensions/CMFreg|CMFreg]]
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]]
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]]
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetryAnalysis]]
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]]
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|MatlabBridge]]
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]]
* [[Documentation/{{documentation/version}}/Extensions/NeedleFinder|NeedleFinder]]
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PETDICOMExtension]]
* [[Documentation/{{documentation/version}}/Extensions/PercutaneousApproachAnalysis|PercutaneousApproachAnalysis]]
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]]
* [[Documentation/{{documentation/version}}/Extensions/VolumeClip|VolumeClip]]
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIABrowser]]

== Extensions removed from Slicer 4.5 ==

* houghTransformCLI: Removed by the original author because it was not needed anymore.

== Extensions renamed ==

* PyDevRemoteDebug -> [[Documentation/{{documentation/version}}/Extensions/DebuggingTools|DebuggingTools]]
* MultidimData -> [[Documentation/{{documentation/version}}/Extensions/Sequences|Sequences]]
* TrackerStabilizer -> [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|Slicer-TrackerStabilizer]]
* AirwaySegmentation -> [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|Slicer-AirwaySegmentation]]

= Other Improvements, Additions & Documentation =

== Optimization ==
* Added support for loading of large images on windows. 
* Reduced the memory footprint by fixing memory leaks
* Sped up by 2x slice rendering when the volume is linearly transformed. 
* Improved reslicing speed of quasi-axis-aligned slices. 
* Sped up annotation ROI display about 10x faster (100ms to 10ms). 
* Improved tractography display performance. 
* Prevent viewers flickering when only few nodes are removed.
* Improved performance of transform widget.

== Transforms ==
* Added support for copy/paste of linear transforms.
* Support saving of any transform to a grid transform. 
* Addressed translation slider instability in rotate first mode. 
* Improved composite transform support. 
* Added support for thin plate spline transforms. 
* Changed default ITK bspline transform writing file format to ITKv4. 
* Addressed display issue for slice intersection display of non-linearly transformed model. 
* Made transforms module translate-rotate first icon nicer.

== DICOM ==
* Improved DICOM browser adding a right click menu allowing delting and exporting to disk patients/studies/series
* Improved support for loading of DICOM referenced datasets.
* Added support for DICOM private dictionary
* Read and apply window/level found in DICOM volumes.
* Added support for Philips DWI datasets
* Fixed loading of DICOM image from files containing special characters.

== Data processing ==
* 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]

== CLI ==
* Added support for transfer of fiducial file to/from CLI modules. 
* Added support for transfer of Hierarchy sub-scene to/from CLI modules. 
* Fixed loading multivolumes produced by CLI modules. 

== Usability ==
* Built-in module categories and extensions categories are listed separately in module selector.
* Allow multi-selection in subject hierarchy.
* Generate high-resolution magnified screenshots for 3D view.

== SubjectHierarchy ==
* Highlight nodes in subject hierarchy referenced by DICOM 
* Added Transforms subject hierarchy plugin 
* Added new [[Documentation/Labs/DICOMExport|DICOM export feature and scalar volume plugin]].  [http://www.na-mic.org/Bug/view.php?id=3163 #3163]
* Added generic folder plugin to subject hierarchy 
* Subject hierarchy nodes automatically created for supported types 
* Added auto-delete subject hierarchy children to Application Settings 
* Added auto-create subject hierarchy option to Application Settings 
* Subject hierarchy tree headers show icons instead of text 
* Fixed subject hierarchy nodes creation when importing old scene  [http://www.na-mic.org/Bug/view.php?id=3902 #3902]
* Fixed volume visibility controls.  [http://www.na-mic.org/Bug/view.php?id=3893 #3893]

== Python scripting ==
* Upgraded from Numpy 1.4.1 to NumPy 1.9.2
* Upgraded from Python 2.7.3 to Python 2.7.10
* Bundled nose python module into the Slicer package.
* Added logging functions for Python. 
* Fixed VTKObservationMixin and added [[Documentation/Nightly/Developers/Python_scripting#How_can_I_access_callData_argument_in_a_VTK_object_observer_callback_function|documentation]].
* Updated IOManager and DICOMWidgets to emit <code>newFileLoaded()</code>.
* Added logging of Python console user input.
* Added accessor for vertex points of models as numpy array. 
* Allow displayable manager to be introspected using python. 

== Editor ==
* Simplify UI using node selector for merge volume. [http://www.na-mic.org/Bug/view.php?id=2958 #2958]
* Warn user when GrowCut effect is attempted with unsupported image type. 
* Added ability to delete only the selected structure. 
* Ensure label map is updated each time a master volume is selected. 
* Improved threshold paint effect to have inclusive ranges  [http://www.na-mic.org/Bug/view.php?id=4066 #4066]
* Remember paint radius when effect are changed  [http://www.na-mic.org/Bug/view.php?id=1853 #1853]
* Reset editor interface when scene is closed. 
* Ensure a related merge volume is selected after a structure deleted.

== Markups ==
* Added measurements between fiducials in right click menu [http://www.na-mic.org/Bug/view.php?id=1898 #1898]
* Added ability to refocus 3d cameras on a fiducial.  [http://www.na-mic.org/Bug/view.php?id=3683 #3683]

== LabelMapVolumeNode ==
* TBD
* Added labelmap node support to subject hierarchy 
* Improved CLI image widget type handling. 

== Slice viewers ==
* Added control to adjust thickness for label map outlines  [http://www.na-mic.org/Bug/view.php?id=2267 #2267]

== DataProbe ==
* Added magnified slice view into DataProbe panel. 

== SliceViewAnnotations ==
* Added orientation marker to slice view annotations. 
* Improved integration of SliceViewAnnotations.  [http://www.na-mic.org/Bug/view.php?id=3943 #3943]

== OpenIGTLink ==
* 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]

== DoubleArrays ==
* Improved loading and saving of measurement files (.mcsv) 

== CastScalarVolume ==
* Improved CastScalarVolume module to support input of type unsigned char, int or long. 

== SceneView ==
* Improved management of data loaded between creation of SceneViews

== Landmark ==
* Added support for landmark refinement 
* Improved LandmarkRegistration plugin loader displaying message if plugin failed to be loaded.

== MultiVolumeImporter ==
* Fixed loading of MGH variable FA multivolume. 

== FiberBundleLabelSelect ==
* Fixed ADD operation for ‘Label to include’.  [http://www.na-mic.org/Bug/view.php?id=4025 #4025]
* Added support for both VTK and VTP input files.

== DTI support ==
* Resolved multithread issue that caused errors with multiple b values.  [http://www.na-mic.org/Bug/view.php?id=3977 #3977]
* Fixed parallel/perpendicular diffusivity on glyphs, interactive seeding line display.  [http://www.na-mic.org/Bug/view.php?id=3857 #3857]
* 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]
* Added logic for propagating color and opacity to fiber hierarchies.  [http://www.na-mic.org/Bug/view.php?id=3925 #3925]
* Added support for Fiber Hierarchies in the Models Module.  [http://www.na-mic.org/Bug/view.php?id=3678 #3678]

== VolumeRendering ==
* Fixed volume rendering not visible when non-volume-rendered volume is frequently changing in the scene. 
* Ensure volume rendering is updated when volume geometry is modified.  [http://www.na-mic.org/Bug/view.php?id=4023 #4023]

== FiberTractMeasurements ==
* TBD
* Added CLI module FiberTractMeasurements allowing to XXXX supporting cluster aggregation.

= For Developers =

== Modules and Extensions ==

* ExtensionWizard
** Added "Enable developer mode" option to ExtensionWizard

* SelfTests
** Allow self tests to set a custom delay for message display

* MRMLNodeComboBox
** Allow qMRMLNodeComboBox base name setting for each node type 
** Added removeAttribute function to MRML node comboboxes and proxy model 
** Multiple node types can be created in qMRMLNodeComboBox 
** Support custom behavior for default actions. 

* MRML Scene introspection
** Added node printself output to node inspector 

* Message logging
** Added vtkInfoMacro

* DICOM
** Package additional DCMTK applications: echoscu, dsr2html, xml2dcm and xml2dsr

* Markups
** Signal end fiducial interaction in 3D 
** Add reusable simple markups widget 

* Module API
** Extend module API with "widgetRepresentationCreationEnabled" property

* Slicerlets
** Allow slicelets and Slicer tests to handle log messages. 

* Units
** Added extra units support: frequency, velocity and intensity.
** Extended Units logic API adding GetDisplayCoefficient() and GetSIPrefixCoefficient() 
** Updated MRMLUnitNode to ensure value to string conversion account for precision. 

* SubjectHierarchy
** Introduced adaptor classes facilitating implementation of python scripted subject hierarchy plugins. 
** Introduced autoDeleteSubjectHierarchyChildren property 

* Editor
** Facilitate re-use of Editor python components in extension (LabelStructureListWidget in 043f398)
** Updated EditUtil API adding function SetUseLabelOutline() to explicitly set label outline state on all Slice nodes

== Slicer Core ==

* IDE integration
** Improve build targets organization in IDE that support folders.
** VisualStudio: Do not build documentation when F7 is pressed.
** Facilitate integration with python IDE allowing minimal 'slicer' module to be imported.

* Build-system
** Add support for Visual Studio 2013.
** Update build system anticipating transition to modern CMake.
** Update MacOSX packaging infrastructure anticipating the signing of package in future release.
** Update code base anticipitating compliance with C++11.
** Remove <code>Slicer_ITKV3_COMPATIBILITY</code> build option.
** Add option <code>Slicer_USE_ITKPython</code> to turn on ITK Python wrapping.
** Removed duplicated code using ITK version of MGHIO.

* Python
** Added support writing scripted modules and widgets as new-style Python classes. 
** Simplify scripted module introducing SlicerPythonCppAPI. 
** Introduced qSlicerScriptedUtils::executeFile() 
** Updated CTK to include new PythonQt C++/Python ownership tracking feature. 
** 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]

* Platform support
** Fix support for 32-bit build allowing use of Slicer on Surface tablet.

* Packaging & Testing infrastructure
** Capturing VTK errors/warnings during testing.
** Update extension build system to report packaging error on CDash.

* Rendering / Visualization
** Add Slicer_VTK_RENDERING_BACKEND configure option

* MRML
** Add support in vtkMRMLNode for multiple references to the same node. 
** Introducing InvokeCustomModifiedEvent. 

* ApplicationLogic
** Added function PropagateLabelVolumeSelection(), PropagateForegroundVolumeSelection() and PropagateBackgroundVolumeSelection()

* VolumeRenderingLogic
** Extend volume rendering logic API adding GetPresetByName function. 

* View management
** Add qMRMLLayoutViewFactory 
** Add utility method to display node in only 1 view 

* DICOM
** [https://github.com/Slicer/Slicer/pull/359 upgraded DCMTK to the latest snapshot DCMTK-3.6.1_20150924]


<gallery caption="Improved Toolkits" widths="350px" heights="250px" perrow="3">

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 -->

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 -->

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 -->

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 -->

Image:Qt-logo.png |Moved from Qt 4.7.4 to Qt 4.8.6

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 -->

Image:DCMTK_logo.png|[https://github.com/Slicer/Slicer/pull/359 Upgraded DCMTK to DCMTK-3.6.1_20150924 snapshot]

</gallery>

== Looking at the Code Changes ==

From a git checkout you can easily see the all the commits since the time of the 4.4.0 release:

 git log v4.4.0..HEAD

To see a summary of your own commits, you could use something like:

 git log v4.4.0..HEAD  --oneline --author=me

see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.

[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]

= Related Projects =
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