Documentation/Nightly/Extensions/lapdMouseBrowser - Revision history

Chribaue: updated website reference to use DOI

2019-07-01T20:38:20Z

updated website reference to use DOI

Chribaue at 22:08, 4 December 2018

2018-12-04T22:08:14Z

Chribaue at 19:10, 4 December 2018

2018-12-04T19:10:53Z

Chribaue: added short module descriptions

2018-12-04T16:52:34Z

added short module descriptions

Chribaue: updated project description

2018-12-04T16:12:13Z

updated project description

Chribaue: added screenshots

2018-12-04T16:08:08Z

added screenshots

Chribaue: added collaborators

2018-12-04T15:33:39Z

added collaborators

Chribaue at 15:16, 4 December 2018

2018-12-04T15:16:08Z

Chribaue at 15:15, 4 December 2018

2018-12-04T15:15:50Z

Chribaue: initial documentation

2018-12-04T15:15:07Z

initial documentation

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
The [https://lapdmouse.iibi.uiowa.edu lapdMouse] Browser was funded in part by
[https://tools.niehs.nih.gov/portfolio/index.cfm/portfolio/grantDetail/grant_number/R01ES023863 NIH grant R01 ES023863]<br>
Authors: Christian Bauer (University of Iowa)<br>
Contributors: Reinhard Beichel (University of Iowa), Melissa Krueger (University of Washington), Robb Glenny (University of Washington)<br>
Contact: <email>lapdmouse@iibi.uiowa.edu</email><br>


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
The [https://lapdmouse.iibi.uiowa.edu Lung Anatomy + Particle Deposition Mouse Archive] (lapdMouse) is a collection of anatomic mouse lung models with aerosol deposition measurements to facilitate modeling and computational toxicology. More detailed information about the available datasets and data files can be found on https://lapdmouse.iibi.uiowa.edu.

'''lapdMouseBrowser''' is an extension for 3D Slicer to download and visualize files from the [https://lapdmouse.iibi.uiowa.edu lapdMouse] data archive. It allows the user to browse through the datasets in the [https://lapdmouse.iibi.uiowa.edu lapdMouse] archive, download them to the local drive, and load them in 3D Slicer. Advantages include:

* Visualize [https://lapdmouse.iibi.uiowa.edu lapdMouse] files not natively supported by 3D Slicer:
** airway tree structure with branch labeling
** aerosol deposition measurements
* Download and visualize a set of commonly used files ("standard file selection") with a single click.
* Pre-configured with suitable visualization parameters and color lookup tables for:
** Volumetric images (aerosol and autofluorescent image data)
** Labelmaps (lungs, lobes, near acini, airway segments)
** Mesh models (airway segments, airway wall deposition)

{{documentation/{{documentation/version}}/module-section|Specify a local storage folder}}

'''lapdMouseBrowser''' stores downloaded files in folder ''./lapdMouse'' by default. If you want to change the default storage directory, close the lapdMouse Data Archive Browser window, change the ''Storage Folder'' using the '''lapdMouseBrowser''' 's 3D Slicer module panel (panel on left side of 3D Slicer main window) and reopen the lapdMouse Data Archive Browse window by clicking ''Show browser''.

{{documentation/{{documentation/version}}/module-section|Download and visualize a standard set of files}}

In the '''lapdMouse Data Archive Browser''' window select on the left side the dataset
you want to load. Then on the right side click ''load standard file selection
in Slicer''.

The "standard" file selection includes files commonly used:

* AerosolSub4.mha (aerosol deposition image volume)
* AutofluorescentSub4.mha (autofluorescent image volume showing anatomical structures)
* Lobes.nrrd (Labelmap for lung lobes)
* AirwayOutlets.vtk (Airway mesh with label assigned to outlets)
* AirwayWallDeposition.vtk (aerosol deposition measurements near the airway wall)

If the files have not yet been downloaded, '''lapdMouseBrowser''' will display the
total size of the files and ask the user to confirm the download. '''Note:''' Some
files in the data archive such as full resolution volumetric images are several GB
in size. Depending on your internet speed, the download might take several
minutes. Files that are available on the local hard drive have a different
status icon and will not have to be downloaded again.

Once the files are locally available, they will be loaded into 3D Slicer with
suitable color lookup tables and default visualization parameters (e.g.
gray-value window). After loading the standard files, 3D Slicer displays the
aerosol deposition image and the airway wall deposition measurements mesh, and
an outline of the lung lobes. The visualization parameters and displayed models
can then be modified using 3D Slicer's standard functionality.

{{documentation/{{documentation/version}}/module-section|Download and visualize a custom set of files}}

If you want to download additional (or other) files for a dataset, select the
file names from the list (use `Ctrl`-key to select multiple at once), and click
`download selected files`. '''lapdMouseBrowser''' will display the total size of
the files and ask the user to confirm the download. After download, they get can
get loaded in 3D Slicer using `load selected files`.





{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
* Source code: https://github.com/lapdMouse/lapdMouseBrowser


{{documentation/{{documentation/version}}/extension-footer}}

@@ Line 92: / Line 92: @@
 {{documentation/{{documentation/version}}/extension-section|Modules}}
-*lapdMouseDBBrowser: Main interface to download and loading lapdMouse files
+*lapdMouseDBBrowser: Main interface to download and load lapdMouse files
 <!--*[[Documentation/{{documentation/version}}/Modules/lapdMouseDBBrowser|lapdMouse Database Browser]] -->
-*lapdMousevisualizer: Create visualizations (models) for lapdMouse files that are not natively supported by Slicer (tree structures, deposition measurement tables etc.)
+*lapdMouseVisualizer: Create visualizations (models) for lapdMouse files that are not natively supported by Slicer (tree structures, deposition measurement tables etc.)
 <!--*[[Documentation/{{documentation/version}}/Modules/ladpMouseVisualizer|lapdMousevisualizer]]-->

@@ Line 9: / Line 9: @@
 {{documentation/{{documentation/version}}/module-introduction-row}}
 Acknowledgments:
-The [https://lapdmouse.iibi.uiowa.edu lapdMouse] Browser was funded in part by
+The [https://doi.org/10.25820/9arg-9w56 lapdMouse] Browser was funded in part by
 [https://tools.niehs.nih.gov/portfolio/index.cfm/portfolio/grantDetail/grant_number/R01ES023863 NIH grant R01 ES023863]<br>
 Authors: Christian Bauer (University of Iowa)<br>
@@ Line 24: / Line 24: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Extension Description}}
-The [https://lapdmouse.iibi.uiowa.edu Lung Anatomy + Particle Deposition Mouse Archive] (lapdMouse) contains anatomically derived lung models and aerosol deposition measurements of mice for modeling and computational toxicology. For more details about available datasets, data representation, other software, and support, please visit https://lapdmouse.iibi.uiowa.edu.
+The [https://doi.org/10.25820/9arg-9w56 Lung Anatomy + Particle Deposition Mouse Archive] (lapdMouse) contains anatomically derived lung models and aerosol deposition measurements of mice for modeling and computational toxicology. For more details about available datasets, data representation, other software, and support, please visit the project web site at https://doi.org/10.25820/9arg-9w56.
-'''lapdMouseBrowser''' is an extension for 3D Slicer to access and visualize files from the [https://lapdmouse.iibi.uiowa.edu lapdMouse] data archive. It allows the user to browse through the datasets in the [https://lapdmouse.iibi.uiowa.edu lapdMouse] archive, download them to the local drive, and load them in 3D Slicer. Advantages include:
+'''lapdMouseBrowser''' is an extension for 3D Slicer to access and visualize files from the [https://doi.org/10.25820/9arg-9w56 lapdMouse] data archive. It allows the user to browse through the datasets in the [https://doi.org/10.25820/9arg-9w56 lapdMouse] archive, download them to the local drive, and load them in 3D Slicer. Advantages include:
-* Visualize [https://lapdmouse.iibi.uiowa.edu lapdMouse] files not natively supported by 3D Slicer:
+* Visualize [https://doi.org/10.25820/9arg-9w56 lapdMouse] files not natively supported by 3D Slicer:
 ** airway tree structure with branch labeling
 ** aerosol deposition measurements

@@ Line 99: / Line 99: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Information for Developers}}
-* Source code: https://github.com/lapdMouse/lapdMouseBrowser
+* Source code: https://github.com/lapdMouse/Slicer-lapdMouseBrowser
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-footer}}
 <!-- ---------------------------- -->

@@ Line 26: / Line 26: @@
 The [https://lapdmouse.iibi.uiowa.edu Lung Anatomy + Particle Deposition Mouse Archive] (lapdMouse) is a collection of anatomic mouse lung models with aerosol deposition measurements to facilitate modeling and computational toxicology. More detailed information about the available datasets and data files can be found on https://lapdmouse.iibi.uiowa.edu.
-'''lapdMouseBrowser''' is an extension for 3D Slicer to download and visualize files from the [https://lapdmouse.iibi.uiowa.edu lapdMouse] data archive. It allows the user to browse through the datasets in the [https://lapdmouse.iibi.uiowa.edu lapdMouse] archive, download them to the local drive, and load them in 3D Slicer. Advantages include:
+'''lapdMouseBrowser''' is an extension for 3D Slicer to access and visualize files from the [https://lapdmouse.iibi.uiowa.edu lapdMouse] data archive. It allows the user to browse through the datasets in the [https://lapdmouse.iibi.uiowa.edu lapdMouse] archive, download them to the local drive, and load them in 3D Slicer. Advantages include:
 * Visualize [https://lapdmouse.iibi.uiowa.edu lapdMouse] files not natively supported by 3D Slicer:
@@ Line 36: / Line 36: @@
 ** Labelmaps (lungs, lobes, near acini, airway segments)
 ** Mesh models (airway segments, airway wall deposition)
 {{documentation/{{documentation/version}}/module-section|Specify a local storage folder}}
 {{documentation/{{documentation/version}}/module-section|Download and visualize a standard set of files}}
@@ Line 68: / Line 74: @@
 an outline of the lung lobes. The visualization parameters and displayed models
 can then be modified using 3D Slicer's standard functionality.
 {{documentation/{{documentation/version}}/module-section|Download and visualize a custom set of files}}
 If you want to download additional (or other) files for a dataset, select the
@@ Line 76: / Line 86: @@
 the files and ask the user to confirm the download. After download, they get can
 get loaded in 3D Slicer using ''load selected files''.
 <!-- ---------------------------- -->

@@ Line 14: / Line 14: @@
 Contributors: Reinhard Beichel (University of Iowa), Melissa Krueger (University of Washington), Robb Glenny (University of Washington)<br>
 Contact: <email>lapdmouse@iibi.uiowa.edu</email><br>
 <!-- ---------------------------- -->

@@ Line 65: / Line 65: @@
 If you want to download additional (or other) files for a dataset, select the
-file names from the list (use `Ctrl`-key to select multiple at once), and click
+file names from the list (use ''Ctrl''-key to select multiple at once), and click
-`download selected files`. '''lapdMouseBrowser''' will display the total size of
+''download selected files''. '''lapdMouseBrowser''' will display the total size of
 the files and ask the user to confirm the download. After download, they get can
 get loaded in 3D Slicer using `load selected files`.