NAMIC Wiki - User contributions [en]

2009 Winter Project Week

2009-01-09T17:46:08Z

Singhsh:

Back to [[Project Events]], [[AHM_2009]], [[Events]]

==Introduction to NA-MIC Project Week==

Please read an introduction about these events [[Project_Events#Introduction|here]].

== Dates.Venue.Registration ==

Please [[AHM_2009#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2009#Agenda|click here for the agenda for AHM 2009 and Project Week]].

==Projects==
Please note:
*Please use the [[2009_Winter_Project_Week_Template|'''2009 Project Week Template''']] to create a page for your project(s)
*[[2008_Summer_Project_Week#Projects|Last Event'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 22-26, 2009
<br><br>

The following is a list of all projects that will be pursued at this meeting. ([[Session notes for the moderators]])

===NA-MIC DBP Roadmap Projects===
Please note that these projects 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|Harvard Roadmap Project: Stochastic Tractography for VCFS]]
##[[2009_Winter_Project_Week:GT_TubularSurfaceSeg|Tubular Surface Segmentation for fiber bundle extraction]] (Vandana Mohan GATech, Allen Tannenbaum GATech, Marek Kubicki BWH, Stephen Aylward Kitware)
##[[2009_Winter_Project_Week_StochasticTractography |Stochastic Tractograhy Tool for Slicer]] (Marek Kubicki BWH, Julien de Siebenthal BWH, Steve Pieper Isomics)
##[[2009_Winter_Project_Week_Slicer3Functioning |Evaluation of basic Slicer 3.0 Functionality from a User Perspective]] (Doug Terry BWH, Marek Kubicki BWH, Sylvain Bouix BWH, Steve Pieper, Wendy Plesniak, Nicole Aucoin)
##[[2009_Winter_Project_Week:DTIGroupAnalysis |Group analysis of DTI fiber bundles]] (Casey Goodlett, Guido Gerig, Marek Kubicki, Sylvain Bouix)
#[[DBP2:UNC:Cortical_Thickness_Roadmap|UNC Roadmap Project: Cortical Thickness Measurement for Autism]]
##[[2009_Winter_Project_Week:LocalCorticalThicknessPipeline|Local Cortical Thickness Pipeline]] (Clement Vachet, Martin Styner, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz)
##[[2009_Winter_Project_Week:RegionalCorticalThicknessPipeline|Regional Cortical Thickness Pipeline]] (Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett)
#[[DBP2:MIND:Roadmap|MIND Roadmap Project: Brain Lesion Analysis in Lupus]]
##[[2009_Winter_Project_Week:HighLevelWizard|Slicer High Level Wizard Project]](Steve Pieper, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LesionAlgorithms|Review of Lesion Algorithms]](Ross Whitaker, Vincent Magnotta, Marcel Prastawa, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LongitudinalLesions|Determine Requirements of Longitudinal Lesion Analyses]](Jeremy Bockholt, Marcel Prastawa, Mark Scully, Andriy Fedorov)
##[[2009_Winter_Project_Week:LesionSegmentationEfficiency|Optimize the new segmentation method for speed, memory use, and multi-threading]](Jeremy Bockholt, Steve Piper, Mark Scully)
#[[DBP2:JHU:Roadmap|JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]
##[[prostateSegmentationAHM2009|Prostate segmentation module for Slicer3]] (Siddharth Vikal, Gabor Fichtinger, Queens University, Katie Hayes, Brigham and Women's Hospital, Yi Gao, Allen Tannenbaum, Georgia Tech)

===Other NA-MIC Projects===
#[[2009_Winter_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA, Steve Pieper and Alex Yarmarkovich Isomics)
#[[2009_Winter_Project_Week_Hageman_UCLANSBrainLab | UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning]] (Nathan Hageman UCLA)
#[[2009_Winter_Project_Week_Hageman_FEMSolverLib | Development of FEM / FVM solver library in ITK/VTK/Python]] (Nathan Hageman UCLA, Vince, Nicole Grosland, Luca, Steve)
#[[2009_Winter_Project_Week_Transform_Management | Transform Management]](Jim Miller)
#[[2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 | Interactive 3D Widgets - Introduce new interactors into Slicer; extensions to current widgets to support Slicer]] (Karthik, Will Schroeder, Nicole Aucoin)
#[[2009_Winter_Project_Week_vtkITK_Pipeline | Using ITK in VTK Pipelines]] (Jim, Steve)
#[[2009_Winter_Project_Week_SlicerLayouts | User Interface Flexible Layouts]] (Wendy, Jim, Steve, Sebastien, Ron)
#[[2009_Winter_Project_Week_Python | Python interface completion and packaging - Fortran and openssl problems]] (Luca, Steve, Demian)
#[[Two-tensor tractography in Slicer using Python and Teem]] (Madeleine Seeland, C-F Westin, Xiaodong Tao)
#[[2009_Winter_Project_Week_Rotation_Tangents | Diffusion Tensor Invariant gradients and rotation tangents in Python and Teem]] (Peter Savadjiev, C-F Westin, Luis Ibanez)
#[[2009_Winter_Project_Week_Tractography_Segmentation | Tractography Segmentation by Nonparametric Bayesian Clustering]] (Xiaogang Wang, C-F Westin)
#[[2009_Winter_Project_Week_Automated_GUI_Testing | KWWidgets and Slicer automated GUI testing ]](Sebastien, Yumin, Interested User: Vince)
#[[2009_Winter_Project_Week_ColorModule | Slicer Colors Module update ]](Nicole)
# [[2009_Winter_Project_Week_MRSI | MRSI Module for Slicer ]] (Bjoern Menze)
#[[Volume Rendering]] (Alex, Curt, Nicholas)
#[[2009_Winter_Project_Week_XND | XNAT Desktop BatchMake integration & Slicer interface]] (Dan Marcus, Stephen Aylward, Wendy Plesniak, Curt Lisle)
#[[2009_Winter_Project_Week_Cortical_Correspondence | Cortical correspondence using DTI]] (Ipek, Martin, Xiaodong)
#[[2009_Winter_Project_Week_Command_Line_Program_Testing |Command Line Program Testing]] (Lorensen, Ron)
#[[2009_Winter_Project_Week_Compiler_Warnings:Slicer3_Graffiti |Compiler Warnings:Slicer3's Graffiti]] (Lorensen, NA-MIC)
#[[2009_Winter_Project_Week_Slicer_VMTK |Vessel Segmentation in Slicer using VMTK]] ([[User:haehn|Daniel Haehn]], [[User:lantiga| Luca Antiga]])
#[[2009_Winter_Project_Week_fMRI_Clustering |Exploring Functional Connectivity in fMRI via Clustering]] (Archana Venkataraman, Marek Kubicki, Polina Golland)
#[[2009_Winter_Project_Week_ChangeTracker |Measuring dynamics of tumor growth in Slicer3 with ChangeTracker]] (Andriy Fedorov, Jim Miller, Alex Yarmarkovich, Wendy Plesniak, Marcel Prastawa)
#[[2009_Winter_Project_Week_GWE_Catalogs |GWE integration with catalog files]] (Marco Ruiz, TBD from XNAT group)
#[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti)
#[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard)
#[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas)
#[[2009_Winter_Project_Week_UtahPlugins | Integration of Utah registration and segmentation methods as Slicer plugins]] (Marcel Prastawa)
#[[2009_Winter_Project_Week_OMTRegistration | DWI to MRI Registration Using Optimat Mass Transport]] (Sylvain Bouix, Ivan Kolesov GATech)
#[[2009_Winter_Project_Week_Event_Broker |Propagating Event Broker through Slicer code base]] (Jim, Steve)
#[[2009_Winter_Project_Week_LungImagingPlatform | Lung Imaging Platform]] (James Ross, Raul San Jose)
#[[2009_Winter_Project_Week_SegmentationAtlases | Brain Atlases for Segmentation]] (Michal Depa, Koen Van Leemput, Mert Rory Sabuncu, Polina Golland)
#[[2009_Winter_Project_Week_ShapePipeline | Particle-based Shape Analysis Pipeline]] (Manasi Datar, Josh Cates, Ross Whitaker, Stephen Aylward, Martin Styner)
#[[2009_Winter_Project_Week_EPI_Correction | EPI Geometric Distortion Correction
]] (Ran Tao, Tom Fletcher, Ross Whitaker)

===External Collaborations===
# [[Iowa Meshing Project 2009]]
##[[Iowa Meshing Tutorial]]
#Wake Forest - Virginia Tech: [[2009_Winter_Project_Week_WFU1 | Move to All Slicer3 Workflow]]
#Georgetown U: [[2009_Winter_Project_Week_NAVRFA | Prototype RF Lesion Ablation Workflow prototyped in Slicer]]
#UNC: [[2009_UNC_HAMMER_WML | MR-image registration and white matter lesion segmentation algorithms to be extended and added to namic kit]]
#[[Stanford SIMBIOS: Whole Body Segmentation for Simulation]]
#[[NCI Evaluating NA-MIC Tools for Image Analysis]]
# [[Lung Lesion Sizing Toolkit]]
# [[MGH Radiation Oncology]]

=== 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]
# Starting Thursday, October 16th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 16: Engineering Infrastructure Projects
#*October 23: Funded External Collaboration Projects
#*November 6: DPB Projects
#*November 20: New Collaborations
#*December 4: Other Projects
#*December 18: Loose Ends
#By December 17, 2008: [[2009_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.
# By December 17, 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)
# FINAL TCON: December 18th 3pm ET to tie loose ends
# 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]].

2009 Winter Project Week Tumor Microenvironment

2009-01-09T17:36:39Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|[http://www.nature.com/nrc/journal/v7/n9/fig_tab/nrc2193_F1.html#figure-title Fig 2.]]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju, Gustavo Leone, Michael Ostrowksi
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

We wanted to investigate the use of Slicer3 for building a microscopy pipeline and integrate some of the modules of our existing pipeline into Slicer. To start off we used the execution model to load our segmentation algorithm through slicer and started working on building a loadable module for slicer.

We got Grid Wizard (Marco) running and set up for our pipeline (need to resolve resource manager issue)

We had discussions (Wendy/Curtis) on annotation capabilities of Slicer3 that will be useful for the tumor microscopy datasets

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Tumor Microenvironment

2009-01-09T17:35:38Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|[http://www.nature.com/nrc/journal/v7/n9/fig_tab/nrc2193_F1.html#figure-title Fig 2.]]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju, Gustavo Leone, Michael Ostrowksi
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

We wanted to investigate the use of Slicer3 for building a microscopy pipeline and integrate some of the modules of our existing pipeline into Slicer. To start off we used the execution model to load our segmentation algorithm through slicer and started working on building a loadable module for slicer.

We got Grid Wizard running and set up for our pipeline (need to resolve resource manager issue)

We had discussions (Wendy/Curtis) on annotation capabilities of Slicer3 that will be useful for the tumor microscopy datasets

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week

2009-01-09T17:33:22Z

Singhsh:

Back to [[Project Events]], [[AHM_2009]], [[Events]]

==Introduction to NA-MIC Project Week==

Please read an introduction about these events [[Project_Events#Introduction|here]].

== Dates.Venue.Registration ==

Please [[AHM_2009#Dates._Venue._Registration| click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2009#Agenda|click here for the agenda for AHM 2009 and Project Week]].

==Projects==
Please note:
*Please use the [[2009_Winter_Project_Week_Template|'''2009 Project Week Template''']] to create a page for your project(s)
*[[2008_Summer_Project_Week#Projects|Last Event'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 22-26, 2009
<br><br>

The following is a list of all projects that will be pursued at this meeting. ([[Session notes for the moderators]])

===NA-MIC DBP Roadmap Projects===
Please note that these projects 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|Harvard Roadmap Project: Stochastic Tractography for VCFS]]
##[[2009_Winter_Project_Week:GT_TubularSurfaceSeg|Tubular Surface Segmentation for fiber bundle extraction]] (Vandana Mohan GATech, Allen Tannenbaum GATech, Marek Kubicki BWH, Stephen Aylward Kitware)
##[[2009_Winter_Project_Week_StochasticTractography |Stochastic Tractograhy Tool for Slicer]] (Marek Kubicki BWH, Julien de Siebenthal BWH, Steve Pieper Isomics)
##[[2009_Winter_Project_Week_Slicer3Functioning |Evaluation of basic Slicer 3.0 Functionality from a User Perspective]] (Doug Terry BWH, Marek Kubicki BWH, Sylvain Bouix BWH, Steve Pieper, Wendy Plesniak, Nicole Aucoin)
##[[2009_Winter_Project_Week:DTIGroupAnalysis |Group analysis of DTI fiber bundles]] (Casey Goodlett, Guido Gerig, Marek Kubicki, Sylvain Bouix)
#[[DBP2:UNC:Cortical_Thickness_Roadmap|UNC Roadmap Project: Cortical Thickness Measurement for Autism]]
##[[2009_Winter_Project_Week:LocalCorticalThicknessPipeline|Local Cortical Thickness Pipeline]] (Clement Vachet, Martin Styner, Heather Cody Hazlett, Marc Niethammer, Ipek Oguz)
##[[2009_Winter_Project_Week:RegionalCorticalThicknessPipeline|Regional Cortical Thickness Pipeline]] (Cedric Mathieu, Clement Vachet, Martin Styner, Heather Cody Hazlett)
#[[DBP2:MIND:Roadmap|MIND Roadmap Project: Brain Lesion Analysis in Lupus]]
##[[2009_Winter_Project_Week:HighLevelWizard|Slicer High Level Wizard Project]](Steve Pieper, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LesionAlgorithms|Review of Lesion Algorithms]](Ross Whitaker, Vincent Magnotta, Marcel Prastawa, Mark Scully, Jeremy Bockholt)
##[[2009_Winter_Project_Week:LongitudinalLesions|Determine Requirements of Longitudinal Lesion Analyses]](Jeremy Bockholt, Marcel Prastawa, Mark Scully, Andriy Fedorov)
##[[2009_Winter_Project_Week:LesionSegmentationEfficiency|Optimize the new segmentation method for speed, memory use, and multi-threading]](Jeremy Bockholt, Steve Piper, Mark Scully)
#[[DBP2:JHU:Roadmap|JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]
##[[prostateSegmentationAHM2009|Prostate segmentation module for Slicer3]] (Siddharth Vikal, Gabor Fichtinger, Queens University, Katie Hayes, Brigham and Women's Hospital, Yi Gao, Allen Tannenbaum, Georgia Tech)

===Other NA-MIC Projects===
#[[2009_Winter_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA, Steve Pieper and Alex Yarmarkovich Isomics)
#[[2009_Winter_Project_Week_Hageman_UCLANSBrainLab | UCLA BrainLab/Slicer Neurosurgery Preoperative Tumor Planning]] (Nathan Hageman UCLA)
#[[2009_Winter_Project_Week_Hageman_FEMSolverLib | Development of FEM / FVM solver library in ITK/VTK/Python]] (Nathan Hageman UCLA, Vince, Nicole Grosland, Luca, Steve)
#[[2009_Winter_Project_Week_Transform_Management | Transform Management]](Jim Miller)
#[[2009_Winter_Project_Week_Interactive_3D_Widgets_In_Slicer3 | Interactive 3D Widgets - Introduce new interactors into Slicer; extensions to current widgets to support Slicer]] (Karthik, Will Schroeder, Nicole Aucoin)
#[[2009_Winter_Project_Week_vtkITK_Pipeline | Using ITK in VTK Pipelines]] (Jim, Steve)
#[[2009_Winter_Project_Week_SlicerLayouts | User Interface Flexible Layouts]] (Wendy, Jim, Steve, Sebastien, Ron)
#[[2009_Winter_Project_Week_Python | Python interface completion and packaging - Fortran and openssl problems]] (Luca, Steve, Demian)
#[[Two-tensor tractography in Slicer using Python and Teem]] (Madeleine Seeland, C-F Westin, Xiaodong Tao)
#[[2009_Winter_Project_Week_Rotation_Tangents | Diffusion Tensor Invariant gradients and rotation tangents in Python and Teem]] (Peter Savadjiev, C-F Westin, Luis Ibanez)
#[[2009_Winter_Project_Week_Tractography_Segmentation | Tractography Segmentation by Nonparametric Bayesian Clustering]] (Xiaogang Wang, C-F Westin)
#[[2009_Winter_Project_Week_Automated_GUI_Testing | KWWidgets and Slicer automated GUI testing ]](Sebastien, Yumin, Interested User: Vince)
#[[2009_Winter_Project_Week_ColorModule | Slicer Colors Module update ]](Nicole)
# [[2009_Winter_Project_Week_MRSI | MRSI Module for Slicer ]] (Bjoern Menze)
#[[Volume Rendering]] (Alex, Curt, Nicholas)
#[[2009_Winter_Project_Week_XND | XNAT Desktop BatchMake integration & Slicer interface]] (Dan Marcus, Stephen Aylward, Wendy Plesniak, Curt Lisle)
#[[2009_Winter_Project_Week_Cortical_Correspondence | Cortical correspondence using DTI]] (Ipek, Martin, Xiaodong)
#[[2009_Winter_Project_Week_Command_Line_Program_Testing |Command Line Program Testing]] (Lorensen, Ron)
#[[2009_Winter_Project_Week_Compiler_Warnings:Slicer3_Graffiti |Compiler Warnings:Slicer3's Graffiti]] (Lorensen, NA-MIC)
#[[2009_Winter_Project_Week_Slicer_VMTK |Vessel Segmentation in Slicer using VMTK]] ([[User:haehn|Daniel Haehn]], [[User:lantiga| Luca Antiga]])
#[[2009_Winter_Project_Week_fMRI_Clustering |Exploring Functional Connectivity in fMRI via Clustering]] (Archana Venkataraman, Marek Kubicki, Polina Golland)
#[[2009_Winter_Project_Week_ChangeTracker |Measuring dynamics of tumor growth in Slicer3 with ChangeTracker]] (Andriy Fedorov, Jim Miller, Alex Yarmarkovich, Wendy Plesniak, Marcel Prastawa)
#[[2009_Winter_Project_Week_GWE_Catalogs |GWE integration with catalog files]] (Marco Ruiz, TBD from XNAT group)
#[[2009_Winter_Project_Week_Gofigure_LevelSet |ITK level set solution for cell segmentation in microscopy datasets]] (part of Gofigure) (Kishore mosaliganti)
#[[2009_Winter_Project_Week_Surface_Processing |ITK surface processing filters: Smoothing, spherical parameterization]] (part of Gofigure) (Alex. Gouaillard)
#[[2009_Winter_Project_Week_Manual_Segmentation_Widgets |VTK widgets for manual segmentation and manual validation of segmentation]] (part of Gofigure) (Arnaud Gelas)
#[[2009_Winter_Project_Week_UtahPlugins | Integration of Utah registration and segmentation methods as Slicer plugins]] (Marcel Prastawa)
#[[2009_Winter_Project_Week_OMTRegistration | DWI to MRI Registration Using Optimat Mass Transport]] (Sylvain Bouix, Ivan Kolesov GATech)
#[[2009_Winter_Project_Week_Event_Broker |Propagating Event Broker through Slicer code base]] (Jim, Steve)
#[[2009_Winter_Project_Week_LungImagingPlatform | Lung Imaging Platform]] (James Ross, Raul San Jose)
#[[2009_Winter_Project_Week_SegmentationAtlases | Brain Atlases for Segmentation]] (Michal Depa, Koen Van Leemput, Mert Rory Sabuncu, Polina Golland)
#[[2009_Winter_Project_Week_ShapePipeline | Particle-based Shape Analysis Pipeline]] (Manasi Datar, Josh Cates, Ross Whitaker, Stephen Aylward, Martin Styner)
#[[2009_Winter_Project_Week_EPI_Correction | EPI Geometric Distortion Correction
]] (Ran Tao, Tom Fletcher, Ross Whitaker)
#[[2009_Winter_Project_Week_Tumor_Microenvironment |Pipeline for Tumor Microenvironment]] (Shantanu Singh)

===External Collaborations===
# [[Iowa Meshing Project 2009]]
##[[Iowa Meshing Tutorial]]
#Wake Forest - Virginia Tech: [[2009_Winter_Project_Week_WFU1 | Move to All Slicer3 Workflow]]
#Georgetown U: [[2009_Winter_Project_Week_NAVRFA | Prototype RF Lesion Ablation Workflow prototyped in Slicer]]
#UNC: [[2009_UNC_HAMMER_WML | MR-image registration and white matter lesion segmentation algorithms to be extended and added to namic kit]]
#[[Stanford SIMBIOS: Whole Body Segmentation for Simulation]]
#[[NCI Evaluating NA-MIC Tools for Image Analysis]]
# [[Lung Lesion Sizing Toolkit]]
# [[MGH Radiation Oncology]]

=== 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]
# Starting Thursday, October 16th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 16: Engineering Infrastructure Projects
#*October 23: Funded External Collaboration Projects
#*November 6: DPB Projects
#*November 20: New Collaborations
#*December 4: Other Projects
#*December 18: Loose Ends
#By December 17, 2008: [[2009_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.
# By December 17, 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)
# FINAL TCON: December 18th 3pm ET to tie loose ends
# 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]].

2009 Winter Project Week Tumor Microenvironment

2009-01-09T17:17:07Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|[http://www.nature.com/nrc/journal/v7/n9/fig_tab/nrc2193_F1.html#figure-title Fig 2.]]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju, Gustavo Leone, Michael Ostrowksi
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

We wanted to investigate the use of Slicer3 for building a microscopy pipeline and integrate some of the modules of our existing pipeline into Slicer. To start off we used the execution model to load our segmentation algorithm through slicer and started working on building a loadable module for slicer.

We got Grid Wizard running and set up for our pipeline (need to resolve resource manager issue)

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Manual Segmentation Widgets

2009-01-09T17:10:58Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[]]
|[[]]
|}

__NOTOC__

===Key Investigators===
* Arnaud Gelas, Harvard Medical School
* Kishore Mosaliganti Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School

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

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

<h1>Objective</h1>

* Test
* run on examples
* Write corresponding IJ paper
* submit to IJ

</div>

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

<h1>Approach, Plan</h1>
* Filters are already implemented
* Code Review with a VTK expert (?)
* Run on some datasets
* Write IJ paper
* Submit

</div>

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

<h1>Progress</h1>
* Filters are already implemented
* Discussion and demonstration with Karthik
* Start using the contour widget and integrating with free line tracer in contour widget in GoFigure
* Still having some problems with Qt-VTK on Mac
</div>

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

</div>

===References===

2009 Winter Project Week Manual Segmentation Widgets

2009-01-09T17:10:31Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[]]
|[[]]
|}

__NOTOC__

===Key Investigators===
* Arnaud Gelas, Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School

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

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

<h1>Objective</h1>

* Test
* run on examples
* Write corresponding IJ paper
* submit to IJ

</div>

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

<h1>Approach, Plan</h1>
* Filters are already implemented
* Code Review with a VTK expert (?)
* Run on some datasets
* Write IJ paper
* Submit

</div>

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

<h1>Progress</h1>
* Filters are already implemented
* Discussion and demonstration with Karthik
* Start using the contour widget and integrating with free line tracer in contour widget in GoFigure
* Still having some problems with Qt-VTK on Mac
</div>

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

</div>

===References===

2009 Winter Project Week Gofigure LevelSet

2009-01-09T16:33:57Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:GoFigureZebrafish2D.png|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:KwWidgetLevelSetSegmentationGUI.png|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* Kishore Mosaliganti, Harvard Medical School
* Arnaud Gelas, Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School
* Luca Antiga, Mario Negri Institute
* Luis Ibanez, Kitware

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

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

<h1>Objective</h1>
* Implement a 3D+t image analysis pipeline for multistain microscopy images
* Use references 1-4 for preprocessing, cell segmentation and tracking in ITK
* Make a submission to Insight Journal

</div>

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

<h1>Approach, Plan</h1>
* First prototype of filters are already implemented
* Code review to be done with an ITK expert (luis/bill/jim?)
* Run on cell datasets and build relevant tests
* Write IJ paper

</div>

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

<h1>Progress</h1>
* Improved code quality by making it more memory and run-time efficient
* Wrote test scripts and examples
* Run on cell datasets and exchanged code with Shantanu, OSU and Luca
* Began writing IJ paper

</div>

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

</div>

===References===
# A. Hyvärinen. Fast and Robust Fixed-Point Algorithms for Independent Component Analysis, IEEE Transactions on Neural Networks 10(3):626-634, 1999.
# M. Leventon, W. Grimson and O. Faugeras. Statistical shape influence in geodesic active contours, Computer Vision and Pattern Recognition, 1, pp. 316-323, 2000.
# Tony Chan and Luminita Vese. An active contour model without edges, International Conference on Scale-Space Theories in Computer Vision, pp. 141-151, 1999.
# Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang and Joel Saltz. Reconstruction of Cellular Biological Structures from Optical Microscopy Data. In IEEE Transactions in Visualization and Computer Graphics, 14 (4), pp. 863-876, July/August 2008.
# 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, G. Leone and M. Ostrowski. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.
# Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley and Stephen TC Wong. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biology, 8:40, 2007.

2009 Winter Project Week Tumor Microenvironment

2009-01-05T19:04:34Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|[http://www.nature.com/nrc/journal/v7/n9/fig_tab/nrc2193_F1.html#figure-title Fig 2.]]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju, Gustavo Leone, Michael Ostrowksi
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Tumor Microenvironment

2009-01-05T19:03:21Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|[http://www.nature.com.proxy.lib.ohio-state.edu/nrc/journal/v7/n9/fig_tab/nrc2193_F1.html#figure-title Fig 2.]]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju, Gustavo Leone, Michael Ostrowksi
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Tumor Microenvironment

2009-01-05T18:14:46Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju, Gustavo Leone, Michael Ostrowksi
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Gofigure LevelSet

2009-01-05T18:01:56Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:GoFigureZebrafish2D.png|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:KwWidgetLevelSetSegmentationGUI.png|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* Kishore Mosaliganti, Harvard Medical School
* Arnaud Gelas, Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School
* Luca Antiga, Mario Negri Institute
* Luis Ibanez, Kitware

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

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

<h1>Objective</h1>
* Implement a 3D+t image analysis pipeline for multistain microscopy images
* Use references 1-4 for preprocessing, cell segmentation and tracking in ITK
* Make a submission to Insight Journal

</div>

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

<h1>Approach, Plan</h1>
* First prototype of filters are already implemented
* Code review to be done with an ITK expert (luis/bill/jim?)
* Run on cell datasets and build relevant tests
* Write IJ paper
* Submit

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
# A. Hyvärinen. Fast and Robust Fixed-Point Algorithms for Independent Component Analysis, IEEE Transactions on Neural Networks 10(3):626-634, 1999.
# M. Leventon, W. Grimson and O. Faugeras. Statistical shape influence in geodesic active contours, Computer Vision and Pattern Recognition, 1, pp. 316-323, 2000.
# Tony Chan and Luminita Vese. An active contour model without edges, International Conference on Scale-Space Theories in Computer Vision, pp. 141-151, 1999.
# Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang and Joel Saltz. Reconstruction of Cellular Biological Structures from Optical Microscopy Data. In IEEE Transactions in Visualization and Computer Graphics, 14 (4), pp. 863-876, July/August 2008.
# 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, G. Leone and M. Ostrowski. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.
# Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley and Stephen TC Wong. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biology, 8:40, 2007.

2009 Winter Project Week Tumor Microenvironment

2009-01-05T17:55:40Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju, Gustavo Leone, Michael Ostrowksi
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Tumor Microenvironment

2009-01-05T17:27:58Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] . Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Tumor Microenvironment

2009-01-05T17:25:29Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Fig 1. Surface rendering of cell nuclei in tissue section of a mouse mammary gland. The dataset was acquired using a Zeiss 510 Meta at 0.14um in-plane and 0.33um between-plane resolution. Endothelial cell nuclei (yellow) were identified using an antibody stain (CD-31). Other cells are marked in blue. ]]
|[[Image:snap3.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] (middle image). Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Tumor Microenvironment

2009-01-05T17:11:06Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|]]
|[[Image:snap3.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2008] (middle image). Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Tumor Microenvironment

2009-01-05T17:10:45Z

Singhsh: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|]]
|[[Image:snap3.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2007] (middle image). Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
* T. Vargo-Gogolal, J. M. Rosen, "Modelling breast cancer: one size does not fit all," Nature Reviews Cancer 7, 659-672, September 2007.
* Mosaliganti,L. Cooper, R. Sharp, R. Machiraju, G. Leone, K. Huang, J. Saltz, "Reconstruction of Cellular Biological Structures from Optical Microscopy Data," Visualization and Computer Graphics, IEEE Transactions on , vol.14, no.4, pp.863-876, July-Aug. 2008

2009 Winter Project Week Tumor Microenvironment

2009-01-05T17:04:38Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|]]
|[[Image:snap3.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors. The goal will be to validate the theories shown as schematic from [Vargo-Gogola 2007] (rightmost image).
</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of [Mosaliganti 2007] (middle image). Then the tessellation based method of the same authors, time permitting. Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore labeling capabilities of Slicer3.

</div>

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

<h1>Progress</h1>

Updated every day of Project Week.

</div>

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

</div>

===References===
*

2009 Winter Project Week Tumor Microenvironment

2009-01-05T16:58:13Z

Singhsh:

File:Snap3.jpg

2009-01-05T16:56:35Z

Singhsh:

2009 Winter Project Week Tumor Microenvironment

2009-01-05T16:47:56Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|]]
|[[Image:Tme_snapshot3.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors.

</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of Mosaliganti et al. Then the tessellation based method of the same authors, time permitting.
Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore preliminary labeling.

</div>

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

<h1>Progress</h1>

Updated every day.

</div>

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

</div>

===References===
*

2009 Winter Project Week Tumor Microenvironment

2009-01-05T16:45:12Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju
* GE Global Research: Jens Rittscher
* BWH: Michael Halle, Steve Pieper, Wendy Plesniak

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for characterizing the tumor microenvironment as observed in the murine breast tumors.

</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework.
Begin with level set methods of Mosaliganti et al. Then the tessellation based method of the same authors, time permitting.
Explore what can be obtained with EMSegement of Slicer3. Compare and contrast all sets of results.
Also, explore preliminary labeling.

</div>

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

<h1>Progress</h1>

Updated every day.

</div>

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

</div>

===References===
*

2009 Winter Project Week Gofigure LevelSet

2009-01-05T16:28:46Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:GoFigureZebrafish2D.png|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:KwWidgetLevelSetSegmentationGUI.png|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* Kishore Mosaliganti, Harvard Medical School
* Arnaud Gelas, Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School

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

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

<h1>Objective</h1>
* Implement a 3D+t image analysis pipeline for multistain microscopy images
* Use references 1-4 for preprocessing, cell segmentation and tracking in ITK
* Make a submission to Insight Journal

</div>

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

<h1>Approach, Plan</h1>
* First prototype of filters are already implemented
* Code review to be done with an ITK expert (luis/bill/jim?)
* Run on cell datasets and build relevant tests
* Write IJ paper
* Submit

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
# A. Hyvärinen. Fast and Robust Fixed-Point Algorithms for Independent Component Analysis, IEEE Transactions on Neural Networks 10(3):626-634, 1999.
# M. Leventon, W. Grimson and O. Faugeras. Statistical shape influence in geodesic active contours, Computer Vision and Pattern Recognition, 1, pp. 316-323, 2000.
# Tony Chan and Luminita Vese. An active contour model without edges, International Conference on Scale-Space Theories in Computer Vision, pp. 141-151, 1999.
# Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang and Joel Saltz. Reconstruction of Cellular Biological Structures from Optical Microscopy Data. In IEEE Transactions in Visualization and Computer Graphics, 14 (4), pp. 863-876, July/August 2008.
# 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, G. Leone and M. Ostrowski. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.
# Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley and Stephen TC Wong. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biology, 8:40, 2007.

File:GoFigureZebrafish2D.png

2009-01-05T16:28:05Z

Singhsh: Slice of a confocal image showing cells

Slice of a confocal image showing cells

2009 Winter Project Week Gofigure LevelSet

2009-01-05T16:14:56Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:KwWidgetLevelSetSegmentationGUI.png|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* Kishore Mosaliganti, Harvard Medical School
* Arnaud Gelas, Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School

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

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

<h1>Objective</h1>
* Implement a 3D+t image analysis pipeline for multistain microscopy images
* Use references 1-4 for preprocessing, cell segmentation and tracking in ITK
* Make a submission to Insight Journal

</div>

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

<h1>Approach, Plan</h1>
* First prototype of filters are already implemented
* Code review to be done with an ITK expert (luis/bill/jim?)
* Run on cell datasets and build relevant tests
* Write IJ paper
* Submit

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
# A. Hyvärinen. Fast and Robust Fixed-Point Algorithms for Independent Component Analysis, IEEE Transactions on Neural Networks 10(3):626-634, 1999.
# M. Leventon, W. Grimson and O. Faugeras. Statistical shape influence in geodesic active contours, Computer Vision and Pattern Recognition, 1, pp. 316-323, 2000.
# Tony Chan and Luminita Vese. An active contour model without edges, International Conference on Scale-Space Theories in Computer Vision, pp. 141-151, 1999.
# Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang and Joel Saltz. Reconstruction of Cellular Biological Structures from Optical Microscopy Data. In IEEE Transactions in Visualization and Computer Graphics, 14 (4), pp. 863-876, July/August 2008.
# 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, G. Leone and M. Ostrowski. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.
# Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley and Stephen TC Wong. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biology, 8:40, 2007.

File:KwWidgetLevelSetSegmentationGUI.png

2009-01-05T16:13:38Z

Singhsh: KWWidgets GUI for segmentation pipeline

KWWidgets GUI for segmentation pipeline

2009 Winter Project Week Gofigure LevelSet

2009-01-05T16:01:09Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|}

__NOTOC__

===Key Investigators===
* Kishore Mosaliganti, Harvard Medical School
* Arnaud Gelas, Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School

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

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

<h1>Objective</h1>
* Implement a 3D+t image analysis pipeline for multistain microscopy images
* Use references 1-4 for preprocessing, cell segmentation and tracking in ITK
* Make a submission to Insight Journal

</div>

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

<h1>Approach, Plan</h1>
* First prototype of filters are already implemented
* Code review to be done with an ITK expert (luis/bill/jim?)
* Run on cell datasets and build relevant tests
* Write IJ paper
* Submit

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
# A. Hyvärinen. Fast and Robust Fixed-Point Algorithms for Independent Component Analysis, IEEE Transactions on Neural Networks 10(3):626-634, 1999.
# M. Leventon, W. Grimson and O. Faugeras. Statistical shape influence in geodesic active contours, Computer Vision and Pattern Recognition, 1, pp. 316-323, 2000.
# Tony Chan and Luminita Vese. An active contour model without edges, International Conference on Scale-Space Theories in Computer Vision, pp. 141-151, 1999.
# Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang and Joel Saltz. Reconstruction of Cellular Biological Structures from Optical Microscopy Data. In IEEE Transactions in Visualization and Computer Graphics, 14 (4), pp. 863-876, July/August 2008.
# 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, G. Leone and M. Ostrowski. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.
# Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley and Stephen TC Wong. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biology, 8:40, 2007.

2009 Winter Project Week Gofigure LevelSet

2009-01-05T15:59:11Z

Singhsh: /* References */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[]]
|[[]]
|}

__NOTOC__

===Key Investigators===
* Kishore Mosaliganti, Harvard Medical School
* Arnaud Gelas, Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School

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

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

<h1>Objective</h1>
* Implement a 3D+t image analysis pipeline for multistain microscopy images
* Use references 1-4 for preprocessing, cell segmentation and tracking in ITK
* Make a submission to Insight Journal

</div>

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

<h1>Approach, Plan</h1>
* First prototype of filters are already implemented
* Code review to be done with an ITK expert (luis/bill/jim?)
* Run on cell datasets and build relevant tests
* Write IJ paper
* Submit

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
# A. Hyvärinen. Fast and Robust Fixed-Point Algorithms for Independent Component Analysis, IEEE Transactions on Neural Networks 10(3):626-634, 1999.
# M. Leventon, W. Grimson and O. Faugeras. Statistical shape influence in geodesic active contours, Computer Vision and Pattern Recognition, 1, pp. 316-323, 2000.
# Tony Chan and Luminita Vese. An active contour model without edges, International Conference on Scale-Space Theories in Computer Vision, pp. 141-151, 1999.
# Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang and Joel Saltz. Reconstruction of Cellular Biological Structures from Optical Microscopy Data. In IEEE Transactions in Visualization and Computer Graphics, 14 (4), pp. 863-876, July/August 2008.
# 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, G. Leone and M. Ostrowski. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.
# Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley and Stephen TC Wong. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biology, 8:40, 2007.

2009 Winter Project Week Gofigure LevelSet

2009-01-05T15:49:21Z

Singhsh: /* Key Investigators */

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[]]
|[[]]
|}

__NOTOC__

===Key Investigators===
* Kishore Mosaliganti, Harvard Medical School
* Arnaud Gelas, Harvard Medical School
* Alexandre Gouaillard, Harvard Medical School

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

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

<h1>Objective</h1>
* Implement a 3D+t image analysis pipeline for multistain microscopy images
* Use references 1-4 for preprocessing, cell segmentation and tracking in ITK
* Make a submission to Insight Journal

</div>

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

<h1>Approach, Plan</h1>
* First prototype of filters are already implemented
* Code review to be done with an ITK expert (luis/bill/jim?)
* Run on cell datasets and build relevant tests
* Write IJ paper
* Submit

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
# Kishore Mosaliganti, Lee Cooper, Richard Sharp, Raghu Machiraju, Gustavo Leone, Kun Huang and Joel Saltz. Reconstruction of Cellular Biological Structures from Optical Microscopy Data. In IEEE Transactions in Visualization and Computer Graphics, 14 (4), pp. 863-876, July/August 2008.
# 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, G. Leone and M. Ostrowski. Special Issue on Medical Image Analysis with Applications in Biology, Journal of Medical Image Analysis, 2008.
# Gang Li, Tianming Liu, Ashley Tarokh, Jingxin Nie, Lei Guo, Andrew Mara, Scott Holley and Stephen TC Wong. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biology, 8:40, 2007.

2009 Winter Project Week Tumor Microenvironment

2009-01-05T06:42:25Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for image analysis techniques for characterizing the tumor microenvironment.

</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
*

File:Tme snapshot2.jpg

2009-01-05T06:40:59Z

Singhsh:

2009 Winter Project Week Tumor Microenvironment

2009-01-05T06:40:37Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:Tme_snapshot2.jpg|thumb|320px|Image2]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for image analysis techniques for characterizing the tumor microenvironment.

</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
*

File:Tme snapshot.jpg

2009-01-05T06:38:40Z

Singhsh:

2009 Winter Project Week Tumor Microenvironment

2009-01-05T06:37:18Z

Singhsh:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|[[Image:image2.jpg|thumb|320px|Image2]]
|[[Image:image3.jpg|thumb|320px|Image3]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh, Raghu Machiraju

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

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

<h1>Objective</h1>

To implement a microscopy image analysis pipeline in Slicer3, specifically tailored for image analysis techniques for characterizing the tumor microenvironment.

</div>

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

<h1>Approach, Plan</h1>

Integrate existing segmentation, validation and labeling pipelines into the Slicer3 framework

</div>

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

<h1>Progress</h1>

</div>

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

</div>

===References===
*

2009 Winter Project Week Tumor Microenvironment

2009-01-04T16:45:33Z

Singhsh: New page: {| |Image1 |Image2 |Image3 |} __NOTOC__ ===Key Investigators=== * The Ohio State Univ...

{|
|[[Image:image1.jpg|thumb|320px|Image1]]
|[[Image:image2.jpg|thumb|320px|Image2]]
|[[Image:image3.jpg|thumb|320px|Image3]]
|}

__NOTOC__

===Key Investigators===
* The Ohio State University: Shantanu Singh

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

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

<h1>Objective</h1>

Objective details

</div>

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

<h1>Approach, Plan</h1>

Approach details

</div>

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

<h1>Progress</h1>

Progress details

</div>

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

</div>

===References===
*