Table of Contents

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{| border="1"
 
{| border="1"
 
|- bgcolor="#abcdef"
 
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! Module Name (click on the entries for a detailed description) !! What it does !! Contributors !! SVN (Y/N)!!CPack (Y/N)!!Dash (Y/N)!!Download
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! Module Name (click on the entries for a detailed description) !! What it does !! Contributors !! SVN?<sup>[1]</sup>!!CPack?<sup>[2]</sup>!!CTest?<sup>[3]</sup>!!Download
 
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|-
 
| [[Registration_page|register_pair]]
 
| [[Registration_page|register_pair]]
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| Segment 2-D & 3-D nuclear images
 
| Segment 2-D & 3-D nuclear images
 
|[[User:Yousef|Yousef Al-Kofahi]]
 
|[[User:Yousef|Yousef Al-Kofahi]]
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|[[Y]]
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|Y
−
|[[Y]]
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|Y
−
|[[Y]]
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|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]
 
| [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]
 
|-
 
|-
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| Tracing of neurons and cell processes
 
| Tracing of neurons and cell processes
 
|[[User:Yousef|Yousef Al-Kofahi]] / [[User:Arun|Arunachalam Narayanaswamy]]
 
|[[User:Yousef|Yousef Al-Kofahi]] / [[User:Arun|Arunachalam Narayanaswamy]]
−
|[[Y]]
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|Y
−
|[[Y]]
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|Y
−
|[[Y]]
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|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]
 
| [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]
 
|-
 
|-
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| Compute Object-level associative features
 
| Compute Object-level associative features
 
|[[User:Yousef|Yousef Al-Kofahi]]
 
|[[User:Yousef|Yousef Al-Kofahi]]
−
|[[Y]]
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|Y
−
|[[Y]]
+
|Y
−
|[[Y]]
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|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]
 
| [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]
 
|-
 
|-
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| Compute nuclear features
 
| Compute nuclear features
 
|[[User:Isaac|Isaac Abbot]] / [[User:Yousef|Yousef Al-Kofahi]]
 
|[[User:Isaac|Isaac Abbot]] / [[User:Yousef|Yousef Al-Kofahi]]
−
|[[Y]]
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|Y
−
|[[Y]]
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|Y
−
|[[Y]]
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|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]
 
| [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]
 
|-
 
|-
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|Automatic training set extraction using fuzzy c-means clustering
 
|Automatic training set extraction using fuzzy c-means clustering
 
|[[User:Yousef|Yousef Al-Kofahi]]
 
|[[User:Yousef|Yousef Al-Kofahi]]
−
|[[Y]]
+
|Y
−
|[[Y]]
+
|Y
−
|[[Y]]
+
|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]
 
| [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]
 
|}
 
|}
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<sup>[1]</sup> Is this module's source code checked into the Farsight subversion repository?
 +
 +
<sup>[2]</sup> Is this module included in the Farsight installer?
 +
 +
<sup>[3]</sup> Does this module utilize CTest to verify that its functionality works properly?

Revision as of 14:44, 17 June 2009

The following tables displays which modules are included in the latest stable release of Farsight.

==

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.

==

Module Name (click on the entries for a detailed description) What it does Contributors SVN?[1] CPack?[2] CTest?[3] Download
register_pair 3D pair-wise Image Registration Charlene Tsai win32 win64
register_joint 3D joint Multi-image Registration Charlene Tsai win32 win64
mosaic_images 3D Image Mosaicing Tool Charlene Tsai win32 win64
mosaic_image_pairs Color-coded Image Mosaic for Inspection Charlene Tsai win32 win64
MontageNavigator GUI Tool to Inspect Mosaics (Montages) Charlene Tsai win32 win64
segment_nuclei Segment 2-D & 3-D nuclear images Yousef Al-Kofahi Y Y N win32 win64
Pattern Analysis Module Clustering & outlier analysis Isaac Abbott, Mark Embrechts win32 win64
render Module for 3-D rendering of segmentation & classification results Arunachalam Narayanaswamy win32 win64
RPITrace3D Tracing of neurons and cell processes Yousef Al-Kofahi / Arunachalam Narayanaswamy Y Y N win32 win64
Object_level_association Compute Object-level associative features Yousef Al-Kofahi Y Y N win32 win64
Features Compute nuclear features Isaac Abbot / Yousef Al-Kofahi Y Y N win32 win64
TissueNets Program Build and analyze tissue graphs Aytekin Vargun win32 win64
trace_editor Computer assisted editing of neuron traces Arunachalam Narayanaswamy, Jon Luisi, Zack Galbreath win32 win64
Vessel Laminae Segmentation Segment "hollow" vessels whose laminae are labeled Arunachalam Narayanaswamy win32 win64
Fuzzy_Clustering Automatic training set extraction using fuzzy c-means clustering Yousef Al-Kofahi Y Y N win32 win64


[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 properly?

Retrieved from "http://farsight-toolkit.ee.uh.edu/wiki/Table_of_Contents"
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