Table of Contents

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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/register_joint.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_joint.exe win64]
 
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| [[Registration_page|mosaic_images]]
 
| [[Registration_page|mosaic_images]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/mosaic_images.exe win32]  [http://www.farsight-toolkit.org/modules/win64/mosaic_images.exe win64]
 
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| [[Registration_page|mosaic_image_pairs]]
 
| [[Registration_page|mosaic_image_pairs]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/mosaic_image_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/mosaic_image_pair.exe win64]
 
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| [[Registration_page|MontageNavigator]]
 
| [[Registration_page|MontageNavigator]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/MontageNavigator.exe win32]  [http://www.farsight-toolkit.org/modules/win64/MontageNavigator.exe win64]
 
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|[[Nuclear Segmentation|segment_nuclei]]
 
|[[Nuclear Segmentation|segment_nuclei]]
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|[[Y]]
 
|[[Y]]
 
|[[Y]]
 
|[[Y]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/segment_nuclei.exe win32]  [http://www.farsight-toolkit.org/modules/win64/segment_nuclei.exe win64]
 
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|[[Pattern Analysis Module]]
 
|[[Pattern Analysis Module]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/svm.zip win32]  [http://www.farsight-toolkit.org/modules/win64/svm.zip win64]
 
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|[[FARSIGHT_Tutorials/5-Label#3D_Rendering|render]]
 
|[[FARSIGHT_Tutorials/5-Label#3D_Rendering|render]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/render.exe win32]  [http://www.farsight-toolkit.org/modules/win64/render.exe win64]
 
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|[[FARSIGHT_Tutorials/5-Label#Trace_Astrocytes|RPITrace3D]]
 
|[[FARSIGHT_Tutorials/5-Label#Trace_Astrocytes|RPITrace3D]]
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|[[Y]]
 
|[[Y]]
 
|[[Y]]
 
|[[Y]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/RPITrace3D.exe win32]  [http://www.farsight-toolkit.org/modules/win64/RPITrace3D.exe win64]
 
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|[[Object_level_association]]
 
|[[Object_level_association]]
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|[[Y]]
 
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|[[Y]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/compute_associative_measures.exe win32]  [http://www.farsight-toolkit.org/modules/win64/compute_associative_measures.exe win64]
 
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|[[Features]]
 
|[[Features]]
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|[[Y]]
 
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/compute_nuclei_features.exe win32]  [http://www.farsight-toolkit.org/modules/win64/compute_nuclei_features.exe win64]
 
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|[[TissueNets Program]]
 
|[[TissueNets Program]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/tissuenets.exe win32]  [http://www.farsight-toolkit.org/modules/win64/tissuenets.exe win64]
 
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|[[Trace_Editor|trace_editor]]
 
|[[Trace_Editor|trace_editor]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/trace_editor.exe win32]  [http://www.farsight-toolkit.org/modules/win64/trace_editor.exe win64]
 
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|[[Vessel Laminae Segmentation]]
 
|[[Vessel Laminae Segmentation]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/vessel_segmentation.exe win32]  [http://www.farsight-toolkit.org/modules/win64/vessel_segmentation.exe win64]
 
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|[[Fuzzy_Clustering]]
 
|[[Fuzzy_Clustering]]
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|[[Y]]
 
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|[[Y]]
 
|[[Y]]
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| [http://www.farsight-toolkit.org/modules/win32/register_pair.exe win32]  [http://www.farsight-toolkit.org/modules/win64/register_pair.exe win64]
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| [http://www.farsight-toolkit.org/modules/win32/run_fuzzy_clustering.exe win32]  [http://www.farsight-toolkit.org/modules/win64/run_fuzzy_clustering.exe win64]
 
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Revision as of 14:42, 16 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(Y/N) CPack (Y/N) Dash(Y/N) 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 Y 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 Y win32 win64
Object_level_association Compute Object-level associative features Yousef Al-Kofahi Y Y Y win32 win64
Features Compute nuclear features Isaac Abbot / Yousef Al-Kofahi Y Y Y 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 Y win32 win64
Retrieved from "http://farsight-toolkit.ee.uh.edu/wiki/Table_of_Contents"
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