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2026-04-19T17:40:40Z
User contributions
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https://www.na-mic.org/w/index.php?title=Farsight_nuclear_segmentation_as_GoFigure_plugin&diff=53952
Farsight nuclear segmentation as GoFigure plugin
2010-06-15T17:57:26Z
<p>Raghav: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
Image:Hippocampus.jpg|Farsight nuclei segmentation<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Harvard Medical School: Arnaud Gelas, Sean Megason<br />
* RPI: Badri Roysam, Raghav Padmanabhan<br />
<br />
== Project ==<br />
<br />
* GoFigure2 http://gofigure2.sourceforge.net<br />
GoFigure2 is a software <br />
<br />
* Farsight http://www.farsight-toolkit.org/wiki/Main_Page<br />
Farsight project is Developing Quantitative Tools for Studying Complex and Dynamic Biological Micro-environments from 4D/5D Microscopy Data<br />
<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
<br />
* Enable GoFigure2 plugin mechanism<br />
* Develop one GoFigure2's plugin from Farsight nuclear segmentation<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
<br />
* Make a simple Image To Image plugin work into GoFigure2<br />
* Download, build and install farsight<br />
* Run Farsight nuclear segmentation as an executable<br />
** Import results into GoFigure2 (see previous project)<br />
* Make a plugin from this application<br />
<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
<br />
* GoFigure2's Image to Image plugins can be <br />
** compiled<br />
** loaded<br />
** ran<br />
* There is one bug when importing back the results of the plugin into GoFigure<br />
<br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>
Raghav
https://www.na-mic.org/w/index.php?title=Seedings_results_comparison&diff=53951
Seedings results comparison
2010-06-15T17:56:47Z
<p>Raghav: /* Key Investigators */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]<br />
</gallery><br />
<br />
==Key Investigators==<br />
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason<br />
* RPI: Badri Roysam, Raghav Padmanabhan<br />
<br />
==Project==<br />
[[File:Seed.png]]<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Objective</h3><br />
* Improve segmentation algorithms initialization for nuclei detection in 3D fluorescent microscopy:<br />
** get a better accuracy,<br />
** improve computation speed.<br />
<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h3>Approach, Plan</h3><br />
* Compare different algorithms,<br />
* Find a measure to evaluate different algorithm results,<br />
* Fusion output of several algorithms.<br />
</div><br />
<div style="width: 40%; float: left;"><br />
<br />
<h3>Progress</h3><br />
* Implemented 3 different algorithms with ITK:<br />
** Tensor voting,<br />
** Hough transform,<br />
** Multi-scale Distance Map weighted Laplacian of Gaussian. <br />
</div><br />
</div><br />
<br />
<div style="width: 97%; float: left;"></div>
Raghav