Latest revision as of 21:23, 16 November 2009

Table of Farsight Modules

Module Name (click on the entries for a detailed description)	What it does	Contributors	SVN?^[1]	CPack?^[2]	CTest?^[3]	Download	Licensing Notes
register_pair	3D pair-wise Image Registration	Charlene Tsai	Y	Y	N	win32 win64	Apache License, Version 2.0
register_joint	3D joint Multi-image Registration	Charlene Tsai	Y	Y	N	win32 win64	Apache License, Version 2.0
mosaic_images	3D Image Mosaicing Tool	Charlene Tsai	Y	Y	N	win32 win64	Apache License, Version 2.0
mosaic_image_pair	Color-coded Image Mosaic for Inspection	Charlene Tsai	Y	Y	N	win32 win64	Apache License, Version 2.0
MontageNavigator	GUI Tool to Inspect Mosaics (Montages)	Charlene Tsai	Y	Y	N	win32 win64	Apache License, Version 2.0
segment_nuclei	Segment 2-D & 3-D nuclear images	Yousef Al-Kofahi	Y	Y	N	win32 win64	the GNU General Public License, version 2.
Pattern Analysis Module	Clustering & outlier analysis	Isaac Abbott, Mark Embrechts	Y	Y	N	win32 win64	Apache License, Version 2.0
render	Module for 3-D rendering of segmentation & classification results	Arunachalam Narayanaswamy	Y	Y	N	win32 win64	Apache License, Version 2.0
RPITrace3D	Tracing of neurons and cell processes	Yousef Al-Kofahi / Arunachalam Narayanaswamy	Y	Y	N	win32 win64	Apache License, Version 2.0
SuperEllipseTrace3D	Tracing blood vessels / neurons in 3D	Alex Tyrrell / Amit Mukherjee	Y	Y	N	win32 win64	Apache License, Version 2.0
Object_level_association	Compute Object-level associative features	Yousef Al-Kofahi	Y	Y	N	win32 win64	the GNU General Public License, version 2.
Features	Compute nuclear features	Isaac Abbot / Yousef Al-Kofahi	Y	Y	N	win32 win64	the GNU General Public License, version 2.
TissueNets Program	Build and analyze tissue graphs	Aytekin Vargun	Y	Y	N	win32 win64	Apache License, Version 2.0
trace_editor	Computer assisted editing of neuron traces	Arunachalam Narayanaswamy, Jon Luisi, Zack Galbreath	Y	Y	N	win32 win64	Apache License, Version 2.0
Vessel Laminae Segmentation	Segment "hollow" vessels whose laminae are labeled	Arunachalam Narayanaswamy	Y	Y	N	win32 win64	Apache License, Version 2.0
NucleusEditor	Segment, display, edit, and validate cell nuclei, generate different views of nuclei data	Isaac Abbot,Yousef Al-Kofahi,Aytekin Vargun	Y	Y	N	win32 win64	the GNU General Public License, version 2.
Fuzzy_Clustering	Automatic training set extraction using fuzzy c-means clustering	Yousef Al-Kofahi	Y	Y	N	win32 win64	Apache License, Version 2.0
Skel_streamline	3D Grayscale Image Skeletonization	Xiaosong Yuan	Y	N	N	[win32] [win64]	Apache License, Version 2.0
MDL-constrained Grayscale Skeletonization	Produce Complexity-constrained Dendritic Backbone and Spine Models	Xiaosong Yuan	Y	N	N	[win32] [win64]	Apache License, Version 2.0
wrapper_itk_pre-processing	Running python-based wrappers for ITK pre-processing algorithms (with GUI)	Adarsh K. Ramasubramonian	Y	N	N	[win32] [win64]	Apache License, Version 2.0
Bio-Formats	Standalone Java library for reading and writing life sciences image file formats.	Curtis Rueden, Kevin Eliceiri	Y	N	N	[win32] [win64]	GPL License

^[1] Is this module's source code checked into the Farsight subversion repository?

^[2] Is this module included in the Farsight installer?

^[3] Does this module utilize CTest to verify that its functionality works as intended?

How to maintain this Table

Instructions for the team: I am trying to make sure that all of the modules that we have developed are:

in the SVN repository
in the CPack installable build
described adequately in a wiki page that is linked (also a tutorial when possible).

We will do this one person at a time, and I will be in contact with each member of the team to get this assembled.

Keep all table entries brief, not to exceed the size of a Tweet (i.e, 140 letters or less). The wiki page will describe the module much more completely.

Don't worry about the order in which modules are listed for now. Eventually, they need to be in some systematic order.

We'll be adding more columns to the table later. Your suggestions are welcome. My main concern is to make sure that a biological user can make sense of the modules and know where to look for more information on how to use them. Another concern is to make sure that external collaborators are well positioned to contribute software modules to farsight in a way that is effective.

Badri.

@@ Line 1: / Line 1: @@
+__TOC__
 The following tables displays which modules are included in [[Special:FarsightDownloads|the latest stable release of Farsight]].
-==
+= Table of Farsight Modules =
-Instructions for the team: I am trying to make sure that all of the modules that we have developed are:
-* in the SVN repository
-* in the CPack installable build
-* described adequately in a wiki page that is linked (also a tutorial when possible).
-We will do this one person at a time, and I will be in contact with each member of the team to get this
-assembled.
-Keep all table entries brief, not to exceed the size of a Tweet (i.e, 140 letters or less). The wiki page will
-describe the module much more completely.
-Don't worry about the order in which modules are listed for now. Eventually, they need to be in some
-systematic order.
-We'll be adding more columns to the table later. Your suggestions are welcome. My main concern
-is to make sure that a biological user can make sense of the modules and know where to look
-for more information on how to use them. Another concern is to make sure that external collaborators
-are well positioned to contribute software modules to farsight in a way that is effective.
-Badri.
-==
 {| border="1"
@@ Line 38: / Line 16: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=register_pair.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=register_pair.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 | [[Registration_page#register_joint|register_joint]]
@@ Line 47: / Line 25: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=register_joint.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=register_joint.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 | [[Registration_page#mosaic_images|mosaic_images]]
@@ Line 56: / Line 34: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=mosaic_images.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=mosaic_images.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 | [[Registration_page#mosaic_image_pair|mosaic_image_pair]]
@@ Line 65: / Line 43: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=mosaic_image_pair.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=mosaic_image_pair.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 | [[Registration_page#MontageNavigator|MontageNavigator]]
@@ Line 74: / Line 52: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=MontageNavigator.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=MontageNavigator.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 |[[Nuclear Segmentation|segment_nuclei]]
@@ Line 83: / Line 61: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=segment_nuclei.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=segment_nuclei.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2].
 |-
 |[[Pattern Analysis Module]]
@@ Line 92: / Line 70: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=svm.zip&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=svm.zip&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 |[[FARSIGHT_Tutorials/5-Label#3D_Rendering|render]]
@@ Line 101: / Line 79: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=render.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=render.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 |[[FARSIGHT_Tutorials/5-Label#Trace_Astrocytes|RPITrace3D]]
@@ Line 110: / Line 88: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=RPITrace3D.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=RPITrace3D.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 |[[SuperEllipseTrace3D]]
@@ Line 119: / Line 97: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=Trace3D.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=Trace3D.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 |[[Object_level_association]]
@@ Line 128: / Line 106: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=compute_associative_measures.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_associative_measures.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2].
 |-
 |[[Features]]
@@ Line 137: / Line 115: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=compute_nuclei_features.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_nuclei_features.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2].
 |-
 |[[TissueNets Program]]
@@ Line 146: / Line 124: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=tissuenets.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=compute_nuclei_features.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 |[[Trace_Editor|trace_editor]]
@@ Line 155: / Line 133: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=trace_editor.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=trace_editor.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 |[[Vessel Laminae Segmentation]]
@@ Line 164: / Line 142: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=vessel_segmentation.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=vessel_segmentation.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 |[[NucleusEditor]]
@@ Line 173: / Line 151: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=NucleusEditor.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=NucleusEditor.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2].
 |-
 |[[Fuzzy_Clustering]]
@@ Line 182: / Line 160: @@
 |N
 | [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=run_fuzzy_clustering.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=run_fuzzy_clustering.exe&submit=Download win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 | [[Program_Instruction#Code Components|Skel_streamline]]
@@ Line 191: / Line 169: @@
 |N
 | [win32]  [win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 |-
 | [[Program_Instruction#Code Components|MDL-constrained Grayscale Skeletonization]]
@@ Line 200: / Line 178: @@
 |N
 | [win32]  [win64]
-|Apache License, Version 2.0
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
+|-
+| [[ITK_Pre-Processing_Algorithm_Wrappers_in_Python|wrapper_itk_pre-processing]]
+| Running python-based wrappers for ITK pre-processing algorithms (with GUI)
+| [[User:Ramasa|Adarsh K. Ramasubramonian]]
+|Y
+|N
+|N
+|[win32]  [win64]
+|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
+|-
+| [[Bio-Formats|Bio-Formats]]
+| Standalone Java library for reading and writing life sciences image file formats.
+| Curtis Rueden, Kevin Eliceiri
+|Y
+|N
+|N
+|[win32]  [win64]
+|[http://www.loci.wisc.edu/ome/formats-license.html GPL License]
 |}
@@ Line 209: / Line 205: @@
 <sup>[3]</sup> Does this module utilize CTest to verify that its functionality works as intended?
+= How to maintain this Table =
+Instructions for the team: I am trying to make sure that all of the modules that we have developed are:
+* in the SVN repository
+* in the CPack installable build
+* described adequately in a wiki page that is linked (also a tutorial when possible).
+We will do this one person at a time, and I will be in contact with each member of the team to get this
+assembled.
+Keep all table entries brief, not to exceed the size of a Tweet (i.e, 140 letters or less). The wiki page will
+describe the module much more completely.
+Don't worry about the order in which modules are listed for now. Eventually, they need to be in some
+systematic order.
+We'll be adding more columns to the table later. Your suggestions are welcome. My main concern
+is to make sure that a biological user can make sense of the modules and know where to look
+for more information on how to use them. Another concern is to make sure that external collaborators
+are well positioned to contribute software modules to farsight in a way that is effective.
+Badri.

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Latest revision as of 21:23, 16 November 2009

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Table of Farsight Modules

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