Difference between revisions of "ITK Spherical Harmonics filter for shape analysis of cell nuclei"

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Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
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Image:cell1.png|Cell Nucleus in the Tumor Microenvironment.
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Image:cell2.png|SPHARM-PDM of nucleus.
 
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==Key Investigators==
 
==Key Investigators==
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* OSU: Liya Ding, Kun Huang, Raghu Machiraju
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* OSU: Shantanu Singh, Raghu Machiraju
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* Harvard Medical School: Sean Megason
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* Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason
  
 
==Project==
 
==Project==
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<h3>Objective</h3>
 
<h3>Objective</h3>
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3D histology stacks are being increasingly used to understand gross anatomical changes and to provide
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valuable educational contexts. Most existing toolkits allow a 2D approach and do not meet the challenges
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* 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.
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posed by 3D histology. ITKv4 can facilitate the realization application level toolkits that will allow for a
 
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sensible registration, segmentation and reconstruction of digital slides depicting various organs and tissue
 
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systems. Modules will be included that will allow for pre-processing (color correction, artifact removal,
 
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etc.), rigid and non-rigid registration, material-based segmentation, and visualization.
 
  
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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we have developed a series of algorithms and
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* Use implementation of SPHARM-PDM [3] as a starting point
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computational pipelines for processing large microscopy images using heterogeneous
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* Evaluate efficacy of itkQuadEdgeMesh to compute other descriptors [4] of nuclear surface
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computing platforms including GPU and CPU/GPU clusters. We will extend ITKv4 by
 
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incorporating algorithm families that will allow for comprehensive processing of light
 
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microscopy images to enable both 2D and 3D digital histology.
 
  
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
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We are creating three different workflows to achieve our goals. These
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* Current system for statistical shape analysis of nuclear morphology uses [3] to generate the representation
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workflows accomplish (i) pre-preprocessing the data, (ii) registration/3D reconstruction
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and segmentation/classification of tissue regions from multi-channel data, (iii) and the
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* With Arnaud Gelas, initiated work on using itkQuadEdgeMesh for generating and representing PDM for nuclei
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visualization of the microstructure.
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* With Manasi Datar, initiated experiments on using particle based correspondence for generating PDMs
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* With Marco Ruiz, used GWE to set up the PDM generation on a large dataset of nuclei
  
 
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<div style="width: 97%; float: left;">
 
<div style="width: 97%; float: left;">
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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.
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2. Trimboli et. al., Pten in stromal fibroblasts suppresses mammary epithelial tumours. Nature 461 (7267) p. 1084-91, 2009
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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)

Latest revision as of 13:54, 25 June 2010

Home < ITK Spherical Harmonics filter for shape analysis of cell nuclei

  • Cell Nucleus in the Tumor Microenvironment.

  • SPHARM-PDM of nucleus.

Key Investigators

  • OSU: Shantanu Singh, Raghu Machiraju
  • Harvard Medical School: Arnaud Gelas, Kishore Mosaliganti, Sean Megason

Project

Objective

  • 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.

Approach, Plan

  • Use implementation of SPHARM-PDM [3] as a starting point
  • Evaluate efficacy of itkQuadEdgeMesh to compute other descriptors [4] of nuclear surface

Progress

  • 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

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)

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