Table of Contents

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__TOC__
 +
 
The following tables displays which modules are included in [[Special:FarsightDownloads|the latest stable release of Farsight]].
 
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"
 
{| border="1"
 
|- bgcolor="#abcdef"
 
|- bgcolor="#abcdef"
−
! Module Name (click on the entries for a detailed description) !! Brief Description !! Contributors !! Comments
+
! 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!!Licensing Notes
 
|-
 
|-
−
| [[fregl]]
+
| [[Registration_page#register_pair|register_pair]]
−
| 3D Registration and Mosaicing
+
| 3D pair-wise Image Registration
 
| [[User:Tsaic|Charlene Tsai]]
 
| [[User:Tsaic|Charlene Tsai]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 
|-
 
|-
−
|[[Nuclear Segmentation]]
+
| [[Registration_page#register_joint|register_joint]]
 +
| 3D joint Multi-image Registration
 +
| [[User:Tsaic|Charlene Tsai]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 +
|-
 +
| [[Registration_page#mosaic_images|mosaic_images]]
 +
| 3D Image Mosaicing Tool
 +
| [[User:Tsaic|Charlene Tsai]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 +
|-
 +
| [[Registration_page#mosaic_image_pair|mosaic_image_pair]]
 +
| Color-coded Image Mosaic for Inspection
 +
| [[User:Tsaic|Charlene Tsai]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 +
|-
 +
| [[Registration_page#MontageNavigator|MontageNavigator]]
 +
| GUI Tool to Inspect Mosaics (Montages)
 +
| [[User:Tsaic|Charlene Tsai]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 +
|-
 +
|[[Nuclear Segmentation|segment_nuclei]]
 
| Segment 2-D & 3-D nuclear images
 
| Segment 2-D & 3-D nuclear images
 
|[[User:Yousef|Yousef Al-Kofahi]]
 
|[[User:Yousef|Yousef Al-Kofahi]]
 +
|Y
 +
|Y
 +
|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://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2].
 
|-
 
|-
 
|[[Pattern Analysis Module]]
 
|[[Pattern Analysis Module]]
 
|Clustering & outlier analysis
 
|Clustering & outlier analysis
 
|Isaac Abbott, Mark Embrechts
 
|Isaac Abbott, Mark Embrechts
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 
|-
 
|-
−
|[[FARSIGHT_Tutorials/5-Label#3D_Rendering|Rendering]]
+
|[[FARSIGHT_Tutorials/5-Label#3D_Rendering|render]]
 
|Module for 3-D rendering of segmentation & classification results
 
|Module for 3-D rendering of segmentation & classification results
 
|[[User:Arun|Arunachalam Narayanaswamy]]
 
|[[User:Arun|Arunachalam Narayanaswamy]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 
|-
 
|-
 
|[[FARSIGHT_Tutorials/5-Label#Trace_Astrocytes|RPITrace3D]]
 
|[[FARSIGHT_Tutorials/5-Label#Trace_Astrocytes|RPITrace3D]]
 
| 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
 +
|Y
 +
|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://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 +
|-
 +
|[[SuperEllipseTrace3D]]
 +
| Tracing blood vessels / neurons in 3D
 +
|[[User:Alex Tyrrell|Alex Tyrrell]] / [[User:Amit|Amit Mukherjee]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 
|-
 
|-
 
|[[Object_level_association]]
 
|[[Object_level_association]]
 
| Compute Object-level associative features
 
| Compute Object-level associative features
 
|[[User:Yousef|Yousef Al-Kofahi]]
 
|[[User:Yousef|Yousef Al-Kofahi]]
 +
|Y
 +
|Y
 +
|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://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2].
 
|-
 
|-
 
|[[Features]]
 
|[[Features]]
 
| 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
 +
|Y
 +
|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://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2].
 
|-
 
|-
 
|[[TissueNets Program]]
 
|[[TissueNets Program]]
 
|Build and analyze tissue graphs
 
|Build and analyze tissue graphs
 
|[[User:Vargun|Aytekin Vargun]]
 
|[[User:Vargun|Aytekin Vargun]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 
|-
 
|-
−
|[[TraceEdit]]
+
|[[Trace_Editor|trace_editor]]
 
|Computer assisted editing of neuron traces
 
|Computer assisted editing of neuron traces
−
|[[User:Arun|Arunachalam Narayanaswamy, Jon Luisi,Zack Galbreath]]
+
|[[User:Arun|Arunachalam Narayanaswamy, Jon Luisi, Zack Galbreath]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 
|-
 
|-
 
|[[Vessel Laminae Segmentation]]
 
|[[Vessel Laminae Segmentation]]
 
|Segment "hollow" vessels whose laminae are labeled  
 
|Segment "hollow" vessels whose laminae are labeled  
 
|[[User:Arun|Arunachalam Narayanaswamy]]
 
|[[User:Arun|Arunachalam Narayanaswamy]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 +
|-
 +
|[[NucleusEditor]]
 +
|Segment, display, edit, and validate cell nuclei, generate different views of nuclei data
 +
|[[User:Vargun|Isaac Abbot,Yousef Al-Kofahi,Aytekin Vargun]]
 +
|Y
 +
|Y
 +
|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]
 +
|[http://www.gnu.org/licenses/old-licenses/gpl-2.0.html the GNU General Public License, version 2].
 +
|-
 +
|[[Fuzzy_Clustering]]
 +
|Automatic training set extraction using fuzzy c-means clustering
 +
|[[User:Yousef|Yousef Al-Kofahi]]
 +
|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://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 +
|-
 +
| [[Program_Instruction#Code Components|Skel_streamline]]
 +
| 3D Grayscale Image Skeletonization
 +
| [[User:Xiaosong|Xiaosong Yuan]]
 +
|Y
 +
|N
 +
|N
 +
| [win32]  [win64]
 +
|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
 +
|-
 +
| [[Program_Instruction#Code Components|MDL-constrained Grayscale Skeletonization]]
 +
| Produce Complexity-constrained Dendritic Backbone and Spine Models
 +
| [[User:Xiaosong|Xiaosong Yuan]]
 +
|Y
 +
|N
 +
|N
 +
| [win32]  [win64]
 +
|[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]
 
|}
 
|}
 +
 +
 +
<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 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.

Latest revision as of 21:23, 16 November 2009

Contents


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

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.

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