Table of Contents
The following tables displays which modules are included in the latest stable release of Farsight.
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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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| 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 | Y | Y | N | win32 win64 |
| register_joint | 3D joint Multi-image Registration | Charlene Tsai | Y | Y | N | win32 win64 |
| mosaic_images | 3D Image Mosaicing Tool | Charlene Tsai | Y | Y | N | win32 win64 |
| mosaic_image_pair | Color-coded Image Mosaic for Inspection | Charlene Tsai | Y | Y | N | win32 win64 |
| MontageNavigator | GUI Tool to Inspect Mosaics (Montages) | Charlene Tsai | Y | Y | N | 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 | Y | Y | N | win32 win64 |
| render | Module for 3-D rendering of segmentation & classification results | Arunachalam Narayanaswamy | Y | Y | N | win32 win64 |
| RPITrace3D | Tracing of neurons and cell processes | Yousef Al-Kofahi / Arunachalam Narayanaswamy | Y | Y | N | win32 win64 |
| SuperEllipseTrace3D | Tracing blood vessels / neurons in 3D | Alex Tyrrell / Amit Mukherjee | 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 | Y | Y | N | win32 win64 |
| trace_editor | Computer assisted editing of neuron traces | Arunachalam Narayanaswamy, Jon Luisi, Zack Galbreath | Y | Y | N | win32 win64 |
| Vessel Laminae Segmentation | Segment "hollow" vessels whose laminae are labeled | Arunachalam Narayanaswamy | Y | Y | N | 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 as intended?
