NAMIC Wiki - User contributions [en]

2008 Winter Project Week Geometry and Topology processing of Meshes

2008-01-08T17:03:48Z

Mosaligk: /* Attendees */

Breakout session on "Geometry and Topology processing of Meshes"
Owner: Alex Gouaillard, Caltech

== Presentations ==

*45 mn Prof. David Gu - Discrete Algorithms for Surface mesh processing
*45 mn Alex Gouaillard - Current and future ITK Implementations (QuadEdge, ...) - Parameterization code in ITK, Decimation/smoothing and more in progress.
*20 mn Luca Antiga - Current and potential uses for vascular modelling applications
*15 mn Interactions

== Attendees ==

<em>Please add your name below, if your plan on attending.</em>

* David xianfeng Gu (?)
* Alex hanfei Gouaillard
* Luca Antiga
* Bill Lorensen
* Sean Megason
* Xiaodong Tao
* william schroeder
* Bob O'Bara
* Jim Miller
* Li Shen
* Kishore Mosaliganti
* Okan Irfanoglu
* Firdaus Janoos

== Presenters ==

=== Professor David Xianfeng GU and/or students (http://www.cs.sunysb.edu/~gu/) ===

Prof. GU will be in China mid-december. Depending on the rapidity of the US embassy in China to give him a visa to go back, he will be able to attend the meeting or not. In the unfortunate case he wouldn't be able to attend, one or two of his postdoc students would be there in replacement.

Ricci flow is a powerful geometric analytic tool, which has been applied to prove Poincare conjecture. Ricci flow is a parabolic system of partial differential equations which acts like the heat equation to spread the curvature of a Riemannian metric evenly over the surface to produce a metric of constant curvature. Computational Ricci flow has been invented and applied for computing hyperbolic structures and conformal surface parameterizations, it is expected to play important roles in both mathematics and engineering fields.

Algorithms for computing conformal structure can be summarized as
*For genus zero surface in the first column, the mapping can be computed using spherical harmonic maps, in paper "Genus Zero Surface Conformal Mapping and Its Application to Brain Surface Mapping". Spherical geometry can be defined on the surface.
*For genus one surface in the second column, the mapping can be computed using holomorphic one forms, in paper "Global Conformal Surface Parameterization". Another algorithm is to use Euclidean Ricci flow, in paper "Conformal Surface Parameterization Using Euclidean Ricci Flow". Euclidean geometry can be defined on the surface.
*For higher genus surfaces in the third column, the mapping can be computed using hyperbolic Ricci flow, in paper "Computing Surface Hyperbolic Structure and Real Projective Structure". Hyperbolic geometry can be defined on the surface.

Applications of conformal geometry in engineering fields are innumerous, the followings are the most directly related ones,
*Graphics: surface global conformal parameterization.
*Medical Imaging: conformal brain mapping and colon flattening.
*Geometric Modeling: manifold splines.
*Vision: Surface matching and recognition.

=== Alex. Hanfei Gouaillard (http://www.itk.org/Wiki/User:Agouaillard) and Arnaud Gelas (http://www.creatis.insa-lyon.fr/~gelas) ===

For the past 5 years, both A.G. have been working on applying gometry and topology processing to medical / biological image processing problems, some of them in collaboration for some with Prof. David GU.

They identified very early that surface processing could only be done rigorously using at least an Half-Edge Structure, and even better in the case of image procesing, a Quad-Edge datastructure. They also concluded from their experiment that, even though C-GAL was the best tool out there to do geometry and topology processing, its license, its complexity, the lack of support of several key platform, and the lack of support for Images was ruling it out for Image processing oriented applications. They decided to go for ITK, and to re-implement whatever would be necessary. It was a long term project, done on spare time, which started around 2002.

Nowadays, the data structure is available under the name itkQuadEdgeMesh and is fairly stable and compliant with existing itkMesh API. The original submission can be read here: http://hdl.handle.net/1926/306. The code is available in ITK since 3.2, if compiled with the USE_REVIEW option. Most of the surface processing algorithms can be more easily implemented on top of Euler operators. Their second work has been to implement those on top of itkQuadEdgeMesh to ease further implementations. The code is available in ITK since 3.4, still with the compilation condition. There is still a lot of algorithms waiting to be transfered in ITK, of which the recent submission of the parameterization code (http://hdl.handle.net/1926/1315) is but a small example.

During this presentation, they will list the features they already have a prototype for and try to give a release timeline. We can expect most of the processing features of VTK to be transfered very soon in ITK, and then some more advanced features to come in. They hope to provide ITK with a complete geometrical and topological toolkit. They dream, in a distant future, to be able to implement an exact kernel in ITK to be able to compute in a robust manner Voronoi tesselations and their duals, Delaunay triangulations.
http://iorich.caltech.edu/guithoughts/wiki/itkQuadEdgeMesh

[[Image:TopologicalArtifact.jpg]]

*A. GOUAILLARD, C. Odet, X. GU, “Computing Shortest Cycles on Discrete Surfaces for Acurate Topological Modifications of Medical Image Isosurfaces”, In Proceedings of IEEE EMBC’05, Shanghai, September 11th-14th 2005.
*A. GOUAILLARD, T. Kanai, C. Odet, X. GU, “Optimal Localization of Topological Artefacts on 3D Meshes”, The 11th Int. Conf. on Geometry and Graphics, 1-5 Aug., 2004, Guangzhou, China.

*A. GELAS, Olivier Bernard, Denis Friboulet, Rémy Prost. "Compactly Supported Radial Basis Functions Collocation Method for Image Segmentation". IEEE Transaction on Image Processing, vol. 16(7), pp.1873--1887 2007.
*A. GELAS, Yutaka Ohtake, Takashi Kanai, Rémy Prost. "Surface Reconstruction Using Radial Basis Functions With Support Adapted to the Medial Axis." Elsevier Computer & Graphics, 2006 (submitted).

[[Image:MultiresolutionRemeshing.jpg]]

*A.GELAS, Joel Schaerer, Olivier Bernard, Denis Friboulet, Patrick Clarysse, Isabelle Magnin, Rémy Prost. "Radial basis functions collocation methods for model based level-set segmentation". IEEE ICIP 2007 Proceedings, vol. 2, pp.237--240, San Antonio, Texa, USA, September 2007.
*A. GELAS, Yutaka Ohtake, Takashi Kanai, Rémy Prost. "Approximation of unorganized point set with composite implicit surface". IEEE ICIP 2006 Proceedings, pp.1217--1220, Atlanta, Georgia, USA, October 2006.
*A. GELAS, Rémy Prost. "Multi-resolution reconstruction of irregularly sampled signals with compactly supported radial basis functions". IEEE ICASSP 2006's Proceedings, vol. 3, pp.388--391, Toulouse, France, May 2006.
*A. GOUAILLARD, A. GELAS, S. Valette, E. Boix and R. Prost, “Curvature-based Adaptive Remeshing for Wavelet-Based Multiresolution 3D Meshes”. In Proc. of International Conference on Image Processing ICIP’05, Genova, September 11th-14th 2005. To appear.
*A. GOUAILLARD, A. GELAS, S. Valette, E. Boix, R. Prost, “Remeshing Algorithm for Multiresolution Prior Model in Segmentation. In Proc. of International Conference on Image Processing, ICIP‘04, Singapore, October 24~27 October 2003, pp. 2753-

=== Luca Antiga (http://villacamozzi.marionegri.it/~luca/) ===

Luca Antiga submitted several vessel detection filters to ITK, and is also in charge of the Vascular Modelling Toolkit (vmtk, http://vmtk.sourceforge.net), developed in collaboration with David Steinman, University of Toronto. In vmtk he is working on the detection and quantification of vessels, as well as on pre- and post-processing for computational fluid dynamics (CFD), aimed at population studies on the relationships between geometry, hemodynamics and physio-pathology of the cardiovascular system. Using vtk so far to represent and handle the vessel representation and further quantification, he will talk about the geometrical problems he is facing (medial axis detection, bifurcation detection, vessel reconstruction, and vessels / branch analysis) and how the tools discussed in this breakout session would solve current problems and allow further investigations on different medical problems.

Using Voronoi/Delaunay a lot, he also witnessed a great improvement in the robustness of the solutions when he changed to an exact kernel. Interested today in Ricci flows and other nice discrete algorithms introduced from abstract mathematics by Prof. GU, he is thinking about moving to itkQuadEdge and itkMesh to implement those algorithms. His dreams would be an exact kernel in ITK, 3-manifolds (volume meshes) / 2-manifolds (surface meshes) algorithms, and ultimately to have computational and differential geometry infrastructure available in ITK. And Python and vmtk in Slicer, but that's another story (we're almost there with that!).

*Piccinelli M, Bacigaluppi S, Boccardi E, Ene-Iordache B, Remuzzi A, Veneziani A, Antiga L Influence of internal carotid artery geometry on aneurysm location and orientation: a computational geometry study. Submitted.
*Thomas JB, Antiga L, Che S, Milner JS, Hangan Steinman DA, Spence JD, Rutt BK and Steinman DA. Variation in the carotid bifurcation geometry of young vs. older adults: Implications for "geometric risk" of atherosclerosis. Stroke, 36(11): 2450-2456, Nov 2005.
*Antiga L, Steinman DA. Robust and objective decomposition and mapping of bifurcating vessels. IEEE Transactions on Medical Imaging, 23(6): 704-713, June 2004.
*Antiga L, Ene-Iordache B and Remuzzi A. Computational geometry for patient-specific reconstruction and meshing of blood vessels from MR and CT angiography. IEEE Transactions on Medical Imaging, 22(5): 674-684, May 2003.
*Antiga L, Ene-Iordache B, Caverni L, Cornalba GP and Remuzzi A. Geometric reconstruction for computational mesh generation of arterial bifurcations from CT angiography. Computerized Medical Imaging and Graphics, 26(4): 227-235, June 2002.

[[Image:VoronoiVortices lowres.png]]
Shape and flow in an intracranial aneurysm.

----

Back to [[AHM_2008]], [[Events]]

2008 Winter Project Week:microslicer 3

2007-12-20T20:33:52Z

Mosaligk:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|Mammary Duct of Mouse ]]
|}

__NOTOC__
===Key Investigators===
* The Ohio State University: Kishore Mosaliganti, Raghu Machiraju
* Kitware: Brad Davis, Stephen Aylward
* BWH: Steve Pieper

<div style="margin: 20px;">

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

<h1>Objective</h1>

We have developed techniques to achieve cell/nuclei segmentations in microscopic images. Often, nuclei and cells appear as overlapping structures and splitting them apart is a non-trivial problem in image analysis. The microscopy modalities of interest include light, confocal and phase-contrast microscopy.

We have also work on characterizing biological micro-structure in terms of micro-components. This helps us to perform tissue segmentations, clonal population segmentation and tracking. Once again, we propose to incorporate such techniques borrowed from material science and spatial statistics into the microscopy image analysis workflows.

The objectives of this project are to port the ITK-based cell segmentation and micro-structure characterization code to Slicer3 framework.

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon using image tessellations and micro-structure characterization algorithms widely used in the material science community. These algorithms help us understand biological organization in terms of component packing densities, arrangements and spatial distributions. The algorithms are detailed in the references provided below. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the microSlicer framework in Slicer3, and implement our current developed code into the Slicer3 framework.
</div>

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

<h1>Progress</h1>
We have currently implemented the cell segmentation algorithm using Geodesics Active Contours and Image-based Voronoi Tessellations in the ITK framework. We have also implemented the microstructure characterization algorithms using the N-Point Correlation functions in ITK. Currently, we are working on building a cell shape model to use in cell segmentations.
</div>

<br style="clear: both;" />

</div>

===References===
* Tensor Classification of N-point Correlation Function features for Histology Tissue Segmentation. K. Mosaliganti, F. Janoos, O. Irfanoglu, R. Ridgway, R. Machiraju, K. Huang, J. Saltz, Gustavo Leone and M. Ostrowski. In review for the Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis.
* Visualization of Cellular Biology Structures from Optical Microscopy Data. K. Mosaliganti, L. Cooper, R. Sharp, R. Machiraju, K. Huang and Gustavo Leone. In review at the IEEE Transactions in Visualization and Computer Graphics.
* Geometry-driven Visualization of Microscopic Structures in Biology. K. Mosaliganti, R. Machiraju, K. Huang and Gustavo Leone. In review at the Workshop on Knowledge-Assisted Visualization, IEEE Visualization Conference, Sacramento, California, 2007.
* Automated Quantification of Colony Growth in Clonogenic Assays. K. Mosaliganti, J. Chen, F. Janoos, R. Machiraju, W. Xia, X. Xu, K. Huang. Workshop on Medical Image Analysis with Applications in Biology, 2007, Piscatway, Rutgers, New Jersey, USA.
* Histology Image Segmentation using the N-Point Correlation Functions. F. Janoos, O. Irfanoglu, K. Mosaliganti, R. Machiraju, K. Huang, P.Wenzel, A. de Bruin, G. Leone. In Proceedings of International Symposium of Biomedical Imaging (ISBI) 2007, Washington DC, USA.

File:Case24-coronal-tensors-edit.png

2007-12-19T21:20:36Z

Mosaligk:

[[http://wiki.na-mic.org/Wiki/index.php/Image:DuctRecon.png]]

File:DuctRecon.png

2007-12-19T21:16:31Z

Mosaligk: Cell reconstruction of a mouse mammary duct

Cell reconstruction of a mouse mammary duct

File:Case24-coronal-tensors-edit.png

2007-12-19T21:15:56Z

Mosaligk:

[[Image:DuctRecon.png]]

2008 Winter Project Week:microslicer 3

2007-12-19T21:10:20Z

Mosaligk: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]
|}

__NOTOC__
===Key Investigators===
* The Ohio State University: Kishore Mosaliganti, Raghu Machiraju
* Kitware: Brad Davis, Stephen Aylward
* BWH: Steve Pieper

<div style="margin: 20px;">

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

<h1>Objective</h1>

We have developed techniques to achieve cell/nuclei segmentations in microscopic images. Often, nuclei and cells appear as overlapping structures and splitting them apart is a non-trivial problem in image analysis. The microscopy modalities of interest include light, confocal and phase-contrast microscopy.

We have also work on characterizing biological micro-structure in terms of micro-components. This helps us to perform tissue segmentations, clonal population segmentation and tracking. Once again, we propose to incorporate such techniques borrowed from material science and spatial statistics into the microscopy image analysis workflows.

The objectives of this project are to port the ITK-based cell segmentation and micro-structure characterization code to Slicer3 framework.

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon using image tessellations and micro-structure characterization algorithms widely used in the material science community. These algorithms help us understand biological organization in terms of component packing densities, arrangements and spatial distributions. The algorithms are detailed in the references provided below. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the microSlicer framework in Slicer3, and implement our current developed code into the Slicer3 framework.
</div>

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

<h1>Progress</h1>
We have currently implemented the cell segmentation algorithm using Geodesics Active Contours and Image-based Voronoi Tessellations in the ITK framework. We have also implemented the microstructure characterization algorithms using the N-Point Correlation functions in ITK. Currently, we are working on building a cell shape model to use in cell segmentations.
</div>

<br style="clear: both;" />

</div>

===References===
* Tensor Classification of N-point Correlation Function features for Histology Tissue Segmentation. K. Mosaliganti, F. Janoos, O. Irfanoglu, R. Ridgway, R. Machiraju, K. Huang, J. Saltz, Gustavo Leone and M. Ostrowski. In review for the Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis.
* Visualization of Cellular Biology Structures from Optical Microscopy Data. K. Mosaliganti, L. Cooper, R. Sharp, R. Machiraju, K. Huang and Gustavo Leone. In review at the IEEE Transactions in Visualization and Computer Graphics.
* Geometry-driven Visualization of Microscopic Structures in Biology. K. Mosaliganti, R. Machiraju, K. Huang and Gustavo Leone. In review at the Workshop on Knowledge-Assisted Visualization, IEEE Visualization Conference, Sacramento, California, 2007.
* Automated Quantification of Colony Growth in Clonogenic Assays. K. Mosaliganti, J. Chen, F. Janoos, R. Machiraju, W. Xia, X. Xu, K. Huang. Workshop on Medical Image Analysis with Applications in Biology, 2007, Piscatway, Rutgers, New Jersey, USA.
* Histology Image Segmentation using the N-Point Correlation Functions. F. Janoos, O. Irfanoglu, K. Mosaliganti, R. Machiraju, K. Huang, P.Wenzel, A. de Bruin, G. Leone. In Proceedings of International Symposium of Biomedical Imaging (ISBI) 2007, Washington DC, USA.

File:CellularReconstruction.png

2007-12-19T21:05:57Z

Mosaligk: Cellular reconstruction of a mouse mammary duct

Cellular reconstruction of a mouse mammary duct

2008 Winter Project Week:microslicer 3

2007-12-19T21:03:06Z

Mosaligk: /* Jan 2007 Project Half Week */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]
|}

__NOTOC__
===Key Investigators===
* The Ohio State University: Kishore Mosaliganti, Raghu Machiraju
* Kitware: Brad Davis, Stephen Aylward
* Harvard: Steve Pieper

<div style="margin: 20px;">

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

<h1>Objective</h1>

We have developed techniques to achieve cell/nuclei segmentations in microscopic images. Often, nuclei and cells appear as overlapping structures and splitting them apart is a non-trivial problem in image analysis. The microscopy modalities of interest include light, confocal and phase-contrast microscopy.

We have also work on characterizing biological micro-structure in terms of micro-components. This helps us to perform tissue segmentations, clonal population segmentation and tracking. Once again, we propose to incorporate such techniques borrowed from material science and spatial statistics into the microscopy image analysis workflows.

The objectives of this project are to port the ITK-based cell segmentation and micro-structure characterization code to Slicer3 framework.

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon using image tessellations and micro-structure characterization algorithms widely used in the material science community. These algorithms help us understand biological organization in terms of component packing densities, arrangements and spatial distributions. The algorithms are detailed in the references provided below. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the microSlicer framework in Slicer3, and implement our current developed code into the Slicer3 framework.
</div>

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

<h1>Progress</h1>
We have currently implemented the cell segmentation algorithm using Geodesics Active Contours and Image-based Voronoi Tessellations in the ITK framework. We have also implemented the microstructure characterization algorithms using the N-Point Correlation functions in ITK. Currently, we are working on building a cell shape model to use in cell segmentations.
</div>

<br style="clear: both;" />

</div>

===References===
* Tensor Classification of N-point Correlation Function features for Histology Tissue Segmentation. K. Mosaliganti, F. Janoos, O. Irfanoglu, R. Ridgway, R. Machiraju, K. Huang, J. Saltz, Gustavo Leone and M. Ostrowski. In review for the Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis.
* Visualization of Cellular Biology Structures from Optical Microscopy Data. K. Mosaliganti, L. Cooper, R. Sharp, R. Machiraju, K. Huang and Gustavo Leone. In review at the IEEE Transactions in Visualization and Computer Graphics.
* Geometry-driven Visualization of Microscopic Structures in Biology. K. Mosaliganti, R. Machiraju, K. Huang and Gustavo Leone. In review at the Workshop on Knowledge-Assisted Visualization, IEEE Visualization Conference, Sacramento, California, 2007.
* Automated Quantification of Colony Growth in Clonogenic Assays. K. Mosaliganti, J. Chen, F. Janoos, R. Machiraju, W. Xia, X. Xu, K. Huang. Workshop on Medical Image Analysis with Applications in Biology, 2007, Piscatway, Rutgers, New Jersey, USA.
* Histology Image Segmentation using the N-Point Correlation Functions. F. Janoos, O. Irfanoglu, K. Mosaliganti, R. Machiraju, K. Huang, P.Wenzel, A. de Bruin, G. Leone. In Proceedings of International Symposium of Biomedical Imaging (ISBI) 2007, Washington DC, USA.

2008 Winter Project Week:microslicer 3

2007-12-19T20:56:00Z

Mosaligk: /* June 2007 Project Week */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]
|}

__NOTOC__
===Key Investigators===
* The Ohio State University: Kishore Mosaliganti, Raghu Machiraju
* Kitware: Brad Davis, Stephen Aylward
* Harvard: Steve Pieper

<div style="margin: 20px;">

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

<h1>Objective</h1>

We have developed techniques to achieve cell/nuclei segmentations in microscopic images. Often, nuclei and cells appear as overlapping structures and splitting them apart is a non-trivial problem in image analysis. The microscopy modalities of interest include light, confocal and phase-contrast microscopy.

We have also work on characterizing biological micro-structure in terms of micro-components. This helps us to perform tissue segmentations, clonal population segmentation and tracking. Once again, we propose to incorporate such techniques borrowed from material science and spatial statistics into the microscopy image analysis workflows.

The objectives of this project are to port the ITK-based cell segmentation and micro-structure characterization code to Slicer3 framework.

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon using image tessellations and micro-structure characterization algorithms widely used in the material science community. These algorithms help us understand biological organization in terms of component packing densities, arrangements and spatial distributions. The algorithms are detailed in the references provided below. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the microSlicer framework in Slicer3, and implement our current developed code into the Slicer3 framework.
</div>

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

<h1>Progress</h1>

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

2008 Winter Project Week:microslicer 3

2007-12-19T20:45:32Z

Mosaligk:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]
|}

__NOTOC__
===Key Investigators===
* The Ohio State University: Kishore Mosaliganti, Raghu Machiraju
* Kitware: Brad Davis, Stephen Aylward
* Harvard: Steve Pieper

<div style="margin: 20px;">

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

<h1>Objective</h1>

We have developed techniques to achieve cell/nuclei segmentations in microscopic images. Often, nuclei and cells appear as overlapping structures and splitting them apart is a non-trivial problem in image analysis. The microscopy modalities of interest include light, confocal and phase-contrast microscopy.

We have also work on characterizing biological micro-structure in terms of micro-components. This helps us to perform tissue segmentations, clonal population segmentation and tracking. Once again, we propose to incorporate such techniques borrowed from material science and spatial statistics into the microscopy image analysis workflows.

The objectives of this project are to port the ITK-based cell segmentation and micro-structure characterization code to Slicer3 framework.

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon using image tessellations and micro-structure characterization algorithms widely used in the material science community. These algorithms help us understand biological organization in terms of component packing densities, arrangements and spatial distributions. The algorithms are detailed in the references provided below. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the microSlicer framework in Slicer3, and implement our current developed code into the Slicer3 framework.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

2008 Winter Project Week:microslicer 3

2007-12-19T20:40:04Z

Mosaligk:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]
|}

__NOTOC__
===Key Investigators===
* The Ohio State University: Kishore Mosaliganti, Raghu Machiraju
* Kitware: Brad Davis, Stephen Aylward
* Harvard: Steve Pieper

<div style="margin: 20px;">

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

<h1>Objective</h1>
We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data.

The objectives of this project are to port the Fast Sweeping and optimal geodesic path tractography code to ITK as well as the code to provide for volumetric segmentation of DW-MRI data.

See our [[Algorithm:GATech:Finsler_Active_Contour_DWI| Project Page]] for more details.

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon using image tessellations and micro-structure characterization algorithms widely used in the material science community. These algorithms help us understand biological organization in terms of component packing densities, arrangements and spatial distributions. The algorithms are detailed in the references provided below. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the microSlicer framework in Slicer3, and implement our current developed code into the Slicer3 framework.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

2008 Winter Project Week:microslicer 3

2007-12-19T20:34:06Z

Mosaligk: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]
|}

__NOTOC__
===Key Investigators===
* The Ohio State University: Kishore Mosaliganti, Raghu Machiraju
* Kitware: Brad Davis, Stephen Aylward
* Harvard: Steve Pieper

<div style="margin: 20px;">

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

<h1>Objective</h1>
We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data.

The objectives of this project are to port the Fast Sweeping and optimal geodesic path tractography code to ITK as well as the code to provide for volumetric segmentation of DW-MRI data.

See our [[Algorithm:GATech:Finsler_Active_Contour_DWI| Project Page]] for more details.

</div>

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

<h1>Approach, Plan </h1>
Our approach is described by the references below. Our challenge is to build the ITK infrastructure (such as new ITK iterators) to support this algorithm. Our main purpose at the Project Week is to collaborate on new algorithms and clinical data to provide the best solutions for our DBP partners.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

2008 Winter Project Week

2007-12-19T20:31:32Z

Mosaligk: /* All Other Projects */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
*Next Project Week is at MIT -- June 23-27, 2008

===DBP Roadmap Projects===
Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)

====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)

====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
*[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)

====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)

===All Other Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#Drafting Human Interface and Slicer Style Guidelines (Wendy Plesniak,Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
#Astronomical coordinate system support (Mike Halle, Doug Alan)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#[[2008_Winter_Project_Week:microslicer_3 | Doing microscopy image analysis with Slicer3]] [The Ohio State University](Kishore Mosaliganti, Raghu Machiraju, Brad Davis,Stephen Aylward, Steve Pieper)
#[[2008_Winter_Project_Week:fmri_image_analysis | fMRI Analysis with Slicer 3]] [The Ohio State University](Firdaus Janoos,Raghu Machiraju, Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# By December 17, 2008: [[2008_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].