From FarsightWiki
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.
