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