NAMIC Wiki - User contributions [en]

Seedings results comparison

2010-06-25T14:06:16Z

Antonin07130:

==Key Investigators==
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason
* RPI: Badri Roysam, Raghav Padmanabhan

==Project==
[[File:Seed.png]]
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Improve segmentation algorithms initialization for nuclei detection in 3D fluorescent microscopy:
** get a better accuracy,
** improve computation speed.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Compare different algorithms,
* Find a measure to evaluate different algorithm results,
* Fusion output of several algorithms.
</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Implemented algorithms in ITK:
** Radial voting,
** Multi-scale Distance Map weighted Laplacian of Gaussian.
* Created a collaboration framework using ITK:
** Set of utilities for input images normalization
** Developed a windowed local maxima filter
* Evaluated and compared output of on synthetic 2D data & 3D Nuclei channel from Megason Lab
** Multi-scale Distance Map weighted Laplacian of Gaussian.
** Radial voting

<h3>Next</h3>
* Implement state of the art seeding algorithms with ITK
** gradient flow tracking
* Evaluate new algorithms

</div>
</div>

==Ressources==
* Source code :
git@github.com:antonin07130/NAMICSeeding.git
We shall use [http://git-scm.com/ git] for version control :
A small introduction to git : [http://sourceforge.net/apps/trac/gofigure2/wiki/GIT here]
* Data set :
Non public
<div style="width: 97%; float: left;">

Seedings results comparison

2010-06-25T04:58:40Z

Antonin07130:

==Key Investigators==
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason
* RPI: Badri Roysam, Raghav Padmanabhan

==Project==
[[File:Seed.png]]
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Improve segmentation algorithms initialization for nuclei detection in 3D fluorescent microscopy:
** get a better accuracy,
** improve computation speed.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Compare different algorithms,
* Find a measure to evaluate different algorithm results,
* Fusion output of several algorithms.
</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Implemented algorithms in ITK:
** Radial voting,
** Multi-scale Distance Map weighted Laplacian of Gaussian.
* Created a collaboration framework using ITK:
** Set of utilities for input images normalization
** Developed a windowed local maxima filter
* Evaluated and compared output of on synthetic 2D data & 3D Nuclei channel from Megason Lab
** Multi-scale Distance Map weighted Laplacian of Gaussian.
** Radial voting

</div>
</div>

==Ressources==
* Source code :
git@github.com:antonin07130/NAMICSeeding.git
We shall use [http://git-scm.com/ git] for version control :
A small introduction to git : [http://sourceforge.net/apps/trac/gofigure2/wiki/GIT here]
* Data set :
Non public
<div style="width: 97%; float: left;">

Seedings results comparison

2010-06-25T04:57:17Z

Antonin07130:

==Key Investigators==
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason
* RPI: Badri Roysam, Raghav Padmanabhan

==Project==
[[File:Seed.png]]
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Improve segmentation algorithms initialization for nuclei detection in 3D fluorescent microscopy:
** get a better accuracy,
** improve computation speed.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Compare different algorithms,
* Find a measure to evaluate different algorithm results,
* Fusion output of several algorithms.
</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Implemented 3 different algorithms in various langages:
** Radial voting,
** Hough transform,
** Multi-scale Distance Map weighted Laplacian of Gaussian.
* Created a collaboration framework using ITK:
** Set of utilities for input images normalization
** Developed a windowed local maxima filter
* Evaluated and compared output of on synthetic 2D data & 3D Nuclei channel from Megason Lab
** Multi-scale Distance Map weighted Laplacian of Gaussian.
** Radial voting

</div>
</div>

==Ressources==
* Source code :
git@github.com:antonin07130/NAMICSeeding.git
We shall use [http://git-scm.com/ git] for version control :
A small introduction to git : [http://sourceforge.net/apps/trac/gofigure2/wiki/GIT here]
* Data set :
Non public
<div style="width: 97%; float: left;">

Seedings results comparison

2010-06-21T17:44:08Z

Antonin07130:

==Key Investigators==
* Harvard Medical School: Antonin Perrot-Audet, Kishore Mosaliganti, Sean Megason
* RPI: Badri Roysam, Raghav Padmanabhan

==Project==
[[File:Seed.png]]
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
* Improve segmentation algorithms initialization for nuclei detection in 3D fluorescent microscopy:
** get a better accuracy,
** improve computation speed.

</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
* Compare different algorithms,
* Find a measure to evaluate different algorithm results,
* Fusion output of several algorithms.
</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Implemented 3 different algorithms with ITK:
** Radial voting,
** Hough transform,
** Multi-scale Distance Map weighted Laplacian of Gaussian.

</div>
</div>

==Ressources==
* Source code :
git@github.com:antonin07130/NAMICSeeding.git
We shall use [http://git-scm.com/ git] for version control :
A small introduction to git : [http://sourceforge.net/apps/trac/gofigure2/wiki/GIT here]
* Data set :
Non public
<div style="width: 97%; float: left;">