3D Slicer Version 3.0 Update for mBIRN

Slides:

Advertisements

Similar presentations

Slicer3 for developers – Sonia Pujol, Ph.D. -1- National Alliance for Medical Image Computing Programming into Slicer3 Sonia Pujol, Ph.D. Surgical Planning.

Advertisements

QueryAtlas Steve Pieper, Greg Brown, David Kennedy, Maryanne Martone, Jyl Boline, Burak Ozyurt, Wendy Plesniak, Michael Halle, Anna Tang, and Florin Talos.

Slicer3: Remote I/O & Informatics Architecture for QueryAtlas & Other Applications 2008 fBIRN AHM.

Interfacing processing and visualization tools: FIPS to Slicer3 and the QueryAtlas.

XCEDE Use Cases 2008 mBIRN AHM San Juan, Puerto Rico.

XCEDE Use Cases: QueryAtlas & other scenarios 2008 fBIRN AHM.

National Alliance for Medical Image Computing © 2010, All Rights Reserved Sonia Pujol, PhD Slicer3Minute Tutorial Sonia.

National Alliance for Medical Image Computing © 2010, ARR Sonia Pujol, PhD Slicer3Minute Tutorial Slicer3 minute tutorial.

Surgical Planning Laboratory Brigham and Women’s Hospital Boston, Massachusetts USA a teaching affiliate of Harvard Medical School 3D Slicer And The NA-MIC.

Function / ROI Viewing in Slicer2 and Slicer3 for fBIRN Data.

© NIH National Center for Image-Guided Therapy, March 2008 IGT Clinical Workshop Non-Rigid, Multi-Modality Image Registration for Thermal Ablation: Non-Rigid,

NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering End-user Platform Steve Pieper Isomics, Inc.

NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering End-user Platform Steve Pieper Isomics, Inc.

All Hands Meeting 2005 Morphometry BIRN - Overview - Scientific Achievements.

NA-MIC National Alliance for Medical Image Computing NAMIC-Kit Update Will Schroeder Jim Miller Bill Lorensen.

Collaborations and Architectures mBIRN Progress at BWH.

-- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium.

NA-MIC National Alliance for Medical Image Computing The NA-MIC Kit National Alliance for Medical Image Computing.

XCEDE Use Cases: QueryAtlas & other scenarios to drive Web Services development 2008 NA-MIC summer project week (developing)

NA-MIC National Alliance for Medical Image Computing XNAT eXtenible aNatomy Archiving Toolkit Steve Pieper, PhD Isomics, Inc. Slides.

3D Slicer: A Free & Open Source Platform For Medical Image Analysis and Visualization Brigham and Women’s Hospital.

NA-MIC National Alliance for Medical Image Computing Why NITRC Matters to NA-MIC Steve Pieper, PhD.

NA-MIC National Alliance for Medical Image Computing Slicer3 and the NA-MIC kit Sonia Pujol, Ph.D. Instructor of Radiology Surgical Planning.

Morphometry BIRN Bruce Rosen, M.D. Ph.D.. Scientific Goal Methods –Multi-site MRI calibration, acquisition –Integrate advanced image analysis and visualization.

-1- 3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing 3D Visualization Sonia Pujol, Ph.D. Surgical.

Jeffrey Yap, PhD Ron Kikinis, MD Wendy Plesniak, PhD -1- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak.

National Alliance for Medical Image Computing Slicer3 Status Update.

March 3, 2005 mBIRN All Hands Meeting Data Provenance Nicole Aucoin.

Surgical Planning Laboratory Brigham and Women’s Hospital Boston, Massachusetts USA a teaching affiliate of Harvard Medical School Overview Ron Kikinis,

2004 All Hands Meeting Morphometry BIRN: Milestones for 2005 Jorge Jovicich PhD Steve Pieper, PhD David Kennedy, PhD.

Pujol S., Plesniak, W. -1- National Alliance for Medical Image Computing Neuroimage Analysis Center Harvard CTSC Slicer3 minute tutorial Sonia Pujol, PhD.

William Schroeder, Ph.D. §, Andy Cedilnik §, Sebastien Barré, Ph.D. §, William Lorensen ‡, James Miller, Ph.D. ‡, Daniel Blezek, Ph.D. ‡ § Kitware Inc.,

BIRN Advantages in Morphometry  Standards for Data Management / Curation File Formats, Database Interfaces, User Interfaces  Uniform Acquisition and.

Sonia Pujol, PhD National Alliance for Medical Image Computing © 2010, ARR.

Clinical Measures Genotype Local Storage BIRN Rack SRB MCAT HID/ XNAT/ LONI DUP Calibration & Analysis Tools GRID Portal Mediator Institution A BIRN Rack.

NA-MIC National Alliance for Medical Image Computing The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as An Open Platform for.

All Hands Meeting 2005 AVI Update Morphometry BIRN Analysis, Visualization, and Interpretation.

NA-MIC National Alliance for Medical Image Computing 3D Slicer and the NA-MIC Kit for IGT Research Steve Pieper, PhD NAC, SPL, NA-MIC,

Spring Meeting 2006 Tensor Atlas Morphometry BIRN Analysis, Visualization, and Interpretation.

Spring Meeting 2007 mBIRN Related Activities In and Around BWH.

NA-MIC National Alliance for Medical Image Computing Isomics, Inc. Steve Pieper.

EMSegmentation in Slicer 3 B. Davis, S. Barre, Y. Yuan, W. Schroeder, P. Golland, K. Pohl.

Neuroinformatics Working Group Update 10/26/2009 H Jeremy Bockholt.

NA-MIC National Alliance for Medical Image Computing Slicer Update Jim Miller, Ph.D. Steve Pieper, Ph.D.

Morphometry BIRN Semi-Automated Shape Analysis (SASHA) JHU (CIS): M. F. Beg, C. Ceritoglu, A. Kolasny, M. I. Miller, R. Yashinski MGH (NMR): B. Fischl;

Jorge Jovicich, Ph.D. Massachusetts General Hospital - Harvard Medical School Biomedical Informatics Research Network Overview Testbeds Morphometry BIRN.

Biomedical Informatics Research Network BIRN Workflow Portal.

Neuroimage Analysis Center An NCRR National Resource Center NAC Engineering Core Steve Pieper, Core PI SPL; Isomics, Inc.

Slicer 3 Ron Kikinis, Steve Pieper. CTK Workshop Heidelberg, June 29/30, 2009 Slicer Goals  Stable, Usable, Cross Platform, End-User Software for Medical.

LONI Pipeline Jagadeeswaran LONI,UCLA. Site PI: Arthur W Toga Director, Laboratory of Neuro Imaging Co-Director, Brain Mapping Center Director, Training.

NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering Data Management Stephen R. Aylward Kitware, Inc.

Sonia Pujol, PhD -1- National Alliance for Medical Image Computing Neuroimage Analysis Center Diffusion Tensor Imaging tutorial Sonia Pujol, Ph.D. Surgical.

NA-MIC National Alliance for Medical Image Computing Non-Interactive Tools Stephen Aylward, Kitware

NA-MIC National Alliance for Medical Image Computing 3D Slicer Version 3.0 and Diffusion MRI Steve Pieper, PhD.

NA-MIC National Alliance for Medical Image Computing NA-MIC Core 2 Update Isomics Steve Pieper Isomics, Inc. NA-MIC Engineering Isomics.

All Hands Meeting 2005 Morphometry BIRN Tool Dissemination.

NA-MIC National Alliance for Medical Image Computing Slicer3 Update

NA-MIC National Alliance for Medical Image Computing Slicer Progress in 2009 Steve Pieper, Ph.D.

NA-MIC National Alliance for Medical Image Computing UCSD / BIRN Coordinating Center NAMIC Group Site PI: Mark H. Ellisman Site Project.

Provenance Work Plans and Deliverables October 2005  Data Provenance information in SRB and HID Test upload to SRB (March) Give DB working group formal.

NA-MIC National Alliance for Medical Image Computing Core 1b – Engineering Data Management Daniel Marcus Washington University.

Biomedical Informatics Research Network BIRN Workflow Portal.

Slicer 101 IGT Edition Haiying Liu, M.S. Nobuhiko Hata, Ph.D.

2007 Project Half Week ITK Registration Parallelization: Develop implementations of ITK registration methods to take advantage of multi-core and multi-processor.

AVI Update Morphometry BIRN

Polina Golland Core 1, MIT

Pipeline Execution Environment

Core 2 Progress Day 1 Salt Lake City

NAMIC Software Development Workshop

Ron Kikinis, MD Professor of Radiology, Harvard Medical School

Presentation transcript:

3D Slicer Version 3.0 Update for mBIRN Analysis, Visualization, and Interpretation

What is Slicer3? Total Rework of 3D Slicer At least 80% of code rewritten New versions of VTK (5.0), ITK (3.2) Improved Look and Feel (KWWidgets) Improved Modularity Analysis routines can be used as plugins or command line executables for batch processing Draws on Multi-Institution Community Kitware, Inc., GE Research, Isomics, Inc., BWH, UCLA, UCSD, UIowa, MIT, GaTech, UNC, U Utah, MGH, UCI, Harvard, WashU… NAC, NCIGT, NA-MIC, mBIRN, fBIRN

Slicer3 Usability Clean, Unified GUI Design Wendy Plesniak (BWH) and Sebastien Barre (Kitware) Developed in Close Collaboration with User Community and Trainers Unified Cross Platform Behavior, Easy Installers Undo/Redo, Tooltips, Drag ‘n’ Drop… New Logo!

mBIRN Slicer Goals Ensure mBIRN Slicer functionality stays current with new Slicer version FreeSurfer Interoperability DTI Analysis and Visualization Provenance QueryAtlas BIRNDUP Protocol Neutral Segmentation (EM Segmenter) Informatics Interoperability (XNAT, Portal, Grid, Workflows)

FreeSurfer FreeSurfer Models and Volumes handled as built-in types Scalar Overlays and Lookup Tables will be Supported

DTI Analysis and Visualization Under Active Development but not yet ready Expected by late 2007 Developed with NA-MIC, NAC, LMI, and NCIGT Applications in Image Guided Neurosurgery will Help Drive Development

Provenance Built in from beginning of Slicer3 Track Cross-Platform Issues Windows (XP and soon Vista) Mac OSX (PPC and X86) Linux (32 and 64 bit) Being Integrated with Slicer3 Execution Model Parameters developed with interactive Slicer environment Modules can run as independent batch jobs on cluster or grid using those parameters

QueryAtlas Leverages FreeSurfer and Informatics Interoperability Interactive Data Exploration for mBIRN and fBIRN Ongoing Ontology Tie-in Work and Workflow Development

BIRNDUP Can be ported to Slicer3 Delayed pending development of mBIRN policy for defacing Command line tools for DICOM Header Deidentification publicly available and documented

Protocol Neurtral Segementation EM Segmenter being ported to Slicer3 by MIT and Kitware Tutorial held January 2007 in Utah Documentation on the Web Additional development ongoing Slicer2 version successfully used in MS Lesion segmentation Included in the current 3D Slicer 2.6 Applied to white matter lesion segmentation in Multiple Sclerosis. MPRAGE and FLAIR Available to support BELL Data courtesy Istvan Csapo, Charles Guttmann, Center for Neurological Imaging, Brigham and Women’s Hospital. Algorithm by Kilian Pohl, MIT/BWH/Isomics

XNAT / Informatics Integration Current Status: Query/Browse for Data at XNAT Site (oasis-brains.org) Download XAR (zip) from XNAT Tell Browser to “Open With…” Slicer3 Images Available for Visualization and Analysis Next Steps Manifest / Data Description files / XCEDE FreeSurfer Datasets, DTI Datasets in XNAT Upload of Processed Data Direct Database Interface (Improve download performance) Generalize for BDR