NAMIC Wiki - User contributions [en]

JPEG2000 and HDF5 Image Readers in ITK

2010-06-25T14:06:24Z

Shantanu: /* Project */

==Key Investigators==
* Harvard Medical School: Kishore Mosaliganti, Sean Megason
* Kitware: Luis Ibanez

==Project==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Add support to ITK for reading very large microscopy datasets that exceed available computer memory. In particular, we are implementing methods to read regions of interest, and multiresolution images of dataset which is assumed to be tiled suitably.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
We are adding support for JPEG2000 files (via [http://www.openjpeg.org/ OpenJpeg]), and will be looking soon at [http://www.hdfgroup.org/HDF5/ HDF5] support.
Requests and suggestions from the community are being gathered at
http://www.itk.org/Wiki/Proposals:JPEG_2000_ImageIO
</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
An initial version of the JPEG2000 support is avalable at:
http://svn.na-mic.org/NAMICSandBox/trunk/JPEG2000ImageIO/

We have joined the development team of Open Jpeg and setup a Dashboard for it at:
http://my.cdash.org/index.php?project=OPENJPEG

The current JPEG2000ImageIO class can

* Read j2k and jp2 images, in 8-bits and 16-bits
* Write j2k and jp2 images, in 8-bits and 16-bits

Update:
* Wrote new tests for mosaicing/tiling R/W of the J2K classes
* Reading tests are passing. Writing needs more work to be done
* Useful contributions from Mathieu Malaterre and Bradley Lowekamp
* Working on an Insight Journal submission of the code

</div>
</div>

<div style="width: 97%; float: left;">

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-25T13:54:28Z

Shantanu: /* Project */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:cell1.png|Cell Nucleus in the Tumor Microenvironment.
Image:cell2.png|SPHARM-PDM of nucleus.
</gallery>

==Key Investigators==
* OSU: Shantanu Singh, Raghu Machiraju
* Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason

==Project==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

* In our recent work[1] on studying the variation of nuclear structure in tumor microenvironments [2], we have used SPHARM-PDM [3] to model 3D nuclear shape. We are interested in using itkQuadEdgeMesh as the mesh representation to this end and will be evaluating the use of this class for our system.

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

<h3>Approach, Plan</h3>
* Use implementation of SPHARM-PDM [3] as a starting point
* Evaluate efficacy of itkQuadEdgeMesh to compute other descriptors [4] of nuclear surface

</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Current system for statistical shape analysis of nuclear morphology uses [3] to generate the representation

* With Arnaud Gelas, initiated work on using itkQuadEdgeMesh for generating and representing PDM for nuclei
* With Manasi Datar, initiated experiments on using particle based correspondence for generating PDMs
* With Marco Ruiz, used GWE to set up the PDM generation on a large dataset of nuclei

</div>

</div>

<div style="width: 97%; float: left;">

1. Shantanu Singh, Sundaresan Raman, Enrico Caserta, Gustavo Leone, Michael Ostrowski, Jens Rittscher, Raghu Machiraju: Analysis of Spatial Variation of Nuclear Morphology in Tissue Microenvironments, 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2010.

2. Trimboli et. al., Pten in stromal fibroblasts suppresses mammary epithelial tumours. Nature 461 (7267) p. 1084-91, 2009

3. Martin Styner, Ipek Oguz, Shun Xu, James J Levitt, Martha E Shenton, Guido Gerig Framework for the Statistical Shape Analysis of Brain Structures using SPHARM-PDM, Insight Journal p. 1-20 (2006)

Microscopy Image Analysis

2010-06-22T18:18:18Z

Shantanu: /* Schedule */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
* Wednesday afternoon - Microscopy Breakout Session ( Location: [http://whereis.mit.edu/?go=32 Kiva])
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Palaniappan Lab- Univ of Missouri
*** 1:40pm: Machiraju Lab- Ohio State Univ
**** Shantanu Singh - Large Scale Analysis of Cellular Phenotypes in the Tumor Microenvironment
**** Liya Ding - Image Analysis of Large Histology Datasets using ITK
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network / President Cosmo Software
** 2:40pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week using your project page
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Liya Ding, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute, CompuCyte Corporation
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Andinet Enquobahrie, Kitware
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.
# Alex Yarmarkovich, Isomics, Inc.
# Curtis Lisle, KnowledgeVis
# Tammy Riklin Raviv, CSAIL, MIT

Microscopy Image Analysis

2010-06-22T18:17:50Z

Shantanu: /* Schedule */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
* Wednesday afternoon - Microscopy Breakout Session ( Location: [http://whereis.mit.edu/?go=32 Kiva])
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Palaniappan Lab- Univ of Missouri
*** 1:40pm: Machiraju Lab- Ohio State Univ
**** Shantanu Singh - Large Scale Analysis of Cellular Phenotypes in the Tumor Microenvironment
**** Liya Ding - ITK Analysis of Large Histology Datasets
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network / President Cosmo Software
** 2:40pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week using your project page
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Liya Ding, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute, CompuCyte Corporation
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Andinet Enquobahrie, Kitware
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.
# Alex Yarmarkovich, Isomics, Inc.
# Curtis Lisle, KnowledgeVis
# Tammy Riklin Raviv, CSAIL, MIT

Microscopy Image Analysis

2010-06-22T18:13:26Z

Shantanu: /* Schedule */

= Open Workshop on Microscopy Image Analysis in ITK and VTK =
This workshop is part of the [[2010_Summer_Project_Week]] at MIT. The goal of this workshop is to foster the growth of a community of scientists interested in microscopy image analysis for biology using ITK and VTK

== Preparation ==
If you would like to participate in this workshop then please:
* Add your name to the "Participants" section below
* Add your project to [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis]] projects list on the main page
* Register for the overall conference from [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here]
* Create a wiki page describing your project following the preparation instructions on the [[2010_Summer_Project_Week#Preparation]] home page and link this to your project listing

== Background ==
Optical microscopy is by far the most common form of imaging in biomedical research due to its high spatial resolution (subcellular), high specificity (molecular in the case of fluorescence), and suitability for use in living specimens. A Google Scholar search for "fluorescence microscopy", only one of several types of optical microscopy, returns 1.7 million articles compared with < 1 million for "MRI". Traditionally, the vast majority of these users of microscopy have performed qualitative analysis on a small number of images, but this is quickly changing. There is increasingly a need to perform quantitative analysis on microscopy images and to perform this analysis on large image sets (>100,000 images). In addition to higher throughput, recent advances in microscopy have made higher dimensional imaging commonplace. Researchers now routinely capture microscopy images over the dimensions of space (x,y,z), time (t), and multiple channels of color (lambda). Due to the large datasets, high dimensions, and complexity of analysis, current approaches to microscopy image analysis relying on Java, Matlab, and “home brew” applications are reaching their limits. We believe that a community based effort centered on developing microscopy-specific algorithms and applications built on the C++ class libraries of VTK and ITK represents the best path forward.

== Focus ==
The focus of this workshop will be on segmentation and tracking of cells in optical microscopy images. Segmentation and tracking of cells represents a very common problem in microscopy image analysis. Although there is a common pipeline for many users (e.g. image preprocessing to remove noise, detection of seeds, detection of cells at single timepoints, tracking movements over time, data analysis) the algorithm parameters and algorithms themselves are often dependent on the specifics of the experimental setup. There is thus a strong need to develop a framework to allow users to choose algorithms and tune parameters to most importantly achieve robust segmentation and secondarily minimize computational cost.

==Format==
The format for this meeting will be as a “track” within the NAMIC Project Week 2010 meeting at MIT in Boston, MA on June 21-25. Participants in this workshop should all have specific coding projects relating to cell segmentation and tracking that they wish to complete within the week. Ideally these projects should be collaborative so as to benefit from the gathering of researchers at the conference. At the beginning of the meeting on Monday, workshop participants will present a 1 slide summary of the goals of their project as part of the overall meeting. This slide will take the form of a templated wiki page. For the rest of the week, workshop participants will sit in a common area and code on their projects. We will also have a microscopy breakout session on Wednesday. These project weeks tend to be quite productive because of the concentration of available expertise at the meeting. During the week we will also break from the coding to have a more formal discussion of our current individual efforts, the needs of the microscopy community, the technical issues of combining and exchanging code, and how we should move forward.

== Schedule ==
* Monday afternoon- 1 slide lightning talk of project planned for the week using your project page
* Wednesday afternoon - Microscopy Breakout Session ( Location: [http://whereis.mit.edu/?go=32 Kiva])
** 1:00pm - 2:20pm: Current efforts (20 minute talks per lab). The goal is to describe the user application you are focussed on, your software approach (demos of software are great), and how others can interface with your efforts.
*** 1:00pm: Megason Lab- Dept of Systems Biology, Harvard
**** Sean Megason - Microscopy image analysis for into imaging of embryogenesis
**** Lydie Souhait - Demo of GoFigure
**** Arnaud Gelas - Interfacing with the Megason Lab
*** 1:20pm: Palaniappan Lab- Univ of Missouri
*** 1:40pm: Machiraju Lab- Ohio State Univ
**** Shantanu Singh - Large Scale Analysis of Cellular Phenotypes in the Tumor Microenvironment
*** 2:00pm: Roysam Lab- Rensselaer Polytechnic Institute
*** 2:20pm: Gouaillard Lab - Singapore Immunology Network / President Cosmo Software
** 2:40pm: Roundtable discussion of standards/interfaces
*** Image file types
*** Input-output interface for segmentation and tracking filters
*** Format for outputted data (e.g. automatic annotations of cell size, intensity, cell type)
*** Greatest common denominator of code: ITK classes, compound filters in ITK, plugins?
*** Common human tasks
**** Manual segmentation and editing of results
**** Visualization of results
** Future directions
* Friday- 1 slide summary of results for the week using your project page
* The rest of the time will be spent coding on projects

== Projects ==
The meat of this workshop is project work. This work should be collaborative to fully take advantage of everyone being together at the conference, to learn other people's approaches, and to flesh out the important needs of microscopy image analysis. If you need help formulating a project please contact Arnaud Gelas (arnaud_gelas@hms.harvard.edu) who can help as a matchmaker. Please list your projects in the [[2010_Summer_Project_Week#Microscopy Image Analysis|Microscopy Image Analysis Project]] section of the main page

== Participants ==
Please add your name to the list if you are interested in participating in this workshop
# Raghu Machiraju, Ohio State University
# Thierry Pecot, Ohio State University
# Shantanu Singh, Ohio State University
# Liya Ding, Ohio State University
# Kannappan Palaniappan, University of Missouri
# Ilker Ersoy, University of Missouri
# Adel Hafiane, ENSI-Bourges, France
# Yousef Al-Kofahi, Rensselaer Polytechnic Institute, CompuCyte Corporation
# Kedar Grama, Rensselaer Polytechnic Institute
# Raghav Padmanabhan, Rensselaer Polytechnic Institute
# Arnaud Gelas, Harvard Medical School
# Kishore Mosaliganti, Harvard Medical School
# Nicolas Rannou, Harvard Medical School
# Antonin Perrot-Audet, Harvard Medical School
# Lydie Souhait, Harvard Medical School
# Sean Megason, Harvard Medical School
# Luis Ibanez, Kitware
# Andinet Enquobahrie, Kitware
# Mathieu Malaterre, CoSMo
# Alex. Gouaillard. A*STAR / CoSMo
# Sonia Pujol. Brigham and Women's Hospital
# Steve Pieper, Isomics, Inc.
# Alex Yarmarkovich, Isomics, Inc.
# Curtis Lisle, KnowledgeVis
# Tammy Riklin Raviv, CSAIL, MIT

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-21T05:27:53Z

Shantanu: /* Project */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:cell1.png|Cell Nucleus in the Tumor Microenvironment.
Image:cell2.png|SPHARM-PDM of nucleus.
</gallery>

==Key Investigators==
* OSU: Shantanu Singh, Raghu Machiraju
* Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason

==Project==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

* In our recent work[1] on studying the variation of nuclear structure in tumor microenvironments [2], we have used SPHARM-PDM [3] to model 3D nuclear shape. We are interested in using itkQuadEdgeMesh as the mesh representation to this end and will be evaluating the use of this class for our system.

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

<h3>Approach, Plan</h3>
* Use implementation of SPHARM-PDM [3] as a starting point
* Evaluate efficacy of itkQuadEdgeMesh to compute other descriptors [4] of nuclear surface

</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Current system for statistical shape analysis of nuclear morphology uses [3] to generate the representation

</div>

</div>

<div style="width: 97%; float: left;">

1. Shantanu Singh, Sundaresan Raman, Enrico Caserta, Gustavo Leone, Michael Ostrowski, Jens Rittscher, Raghu Machiraju: Analysis of Spatial Variation of Nuclear Morphology in Tissue Microenvironments, 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2010.

2. Trimboli et. al., Pten in stromal fibroblasts suppresses mammary epithelial tumours. Nature 461 (7267) p. 1084-91, 2009

3. Martin Styner, Ipek Oguz, Shun Xu, James J Levitt, Martha E Shenton, Guido Gerig Framework for the Statistical Shape Analysis of Brain Structures using SPHARM-PDM, Insight Journal p. 1-20 (2006)

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-21T05:12:36Z

Shantanu: /* Project */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:cell1.png|Cell Nucleus in the Tumor Microenvironment.
Image:cell2.png|SPHARM-PDM of nucleus.
</gallery>

==Key Investigators==
* OSU: Shantanu Singh, Raghu Machiraju
* Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason

==Project==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

* In our recent work[1] on studying the variation of nuclear structure in tumor microenvironments [2], we have used SPHARM-PDM [3] to model 3D nuclear shape. We are interested in using itkQuadEdgeMesh as the mesh representation to this end and will be evaluating the use of this class for our system.

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

<h3>Approach, Plan</h3>
* Use implementation of SPHARMS-PDM [3] as a starting point
* Evaluate efficacy of itkQuadEdgeMesh to compute other descriptors [4] of nuclear surface

</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Current system for statistical shape analysis of nuclear morphology uses [3] to generate the representation

</div>

</div>

<div style="width: 97%; float: left;">

1. Shantanu Singh, Sundaresan Raman, Enrico Caserta, Gustavo Leone, Michael Ostrowski, Jens Rittscher, Raghu Machiraju: Analysis of Spatial Variation of Nuclear Morphology in Tissue Microenvironments, 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2010.

2. Trimboli et. al., Pten in stromal fibroblasts suppresses mammary epithelial tumours. Nature 461 (7267) p. 1084-91, 2009

3. Martin Styner, Ipek Oguz, Shun Xu, James J Levitt, Martha E Shenton, Guido Gerig Framework for the Statistical Shape Analysis of Brain Structures using SPHARM-PDM, Insight Journal p. 1-20 (2006)

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-21T05:09:33Z

Shantanu: /* Project */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:cell1.png|Cell Nucleus in the Tumor Microenvironment.
Image:cell2.png|SPHARM-PDM of nucleus.
</gallery>

==Key Investigators==
* OSU: Shantanu Singh, Raghu Machiraju
* Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason

==Project==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

* In our recent work[1] on studying the variation of nuclear structure in tumor microenvironments [2], we have used SPHARM-PDM [3] to model 3D nuclear shape. We are interested in using itkQuadEdgeMesh as the mesh representation to this end and will be evaluating the use of this class for our system.

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

<h3>Approach, Plan</h3>
* Use implementation of spherical harmonics in [[ Algorithm:UNC:Shape_Analysis ]] as a starting point

</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>

</div>

<div style="width: 97%; float: left;">

1. Shantanu Singh, Sundaresan Raman, Enrico Caserta, Gustavo Leone, Michael Ostrowski, Jens Rittscher, Raghu Machiraju: Analysis of Spatial Variation of Nuclear Morphology in Tissue Microenvironments, 7th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2010.
2. Trimboli et. al., Pten in stromal fibroblasts suppresses mammary epithelial tumours. Nature 461 (7267) p. 1084-91, 2009
3. Martin Styner, Ipek Oguz, Shun Xu, James J Levitt, Martha E Shenton, Guido Gerig Framework for the Statistical Shape Analysis of Brain Structures using SPHARM-PDM, Insight Journal p. 1-20 (2006)

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-16T17:36:56Z

Shantanu: /* Project */

File:Cell1.png

2010-06-16T17:36:18Z

Shantanu:

File:Cell2.png

2010-06-16T17:36:01Z

Shantanu:

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-16T17:34:43Z

Shantanu:

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-16T17:30:13Z

Shantanu: /* Project */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* OSU: Shantanu Singh, Raghu Machiraju
* Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason

==Project==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

* Implementation of spherical harmonics using itkQuadEdgeMesh.

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

<h3>Approach, Plan</h3>
* Use implementation of spherical harmonics in [[ Algorithm:UNC:Shape_Analysis ]] as a starting point
*

</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-16T17:22:31Z

Shantanu: /* Project */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* OSU: Shantanu Singh, Raghu Machiraju
* Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason

==Project==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

Implementation of spherical harmonics using itkQuadEdgeMesh

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

<h3>Approach, Plan</h3>

</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

ITK Spherical Harmonics filter for shape analysis of cell nuclei

2010-06-16T17:18:13Z

Shantanu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* OSU: Shantanu Singh, Raghu Machiraju
* Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason

==Project==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

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

<h3>Approach, Plan</h3>

</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">