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Mouse Brain Atlas Meeting

Mouse Brain Atlas Meeting. Use cases e.g. identify genes at a location, and expressing cells; supporting workflows: data publication and registration, visualization, annotation (incl. collaborative delineation), single-slice, cross-slice and cross-scale query, integration at various levels…

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Mouse Brain Atlas Meeting

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  1. Mouse Brain Atlas Meeting • Use cases • e.g. identify genes at a location, and expressing cells; • supporting workflows: data publication and registration, visualization, annotation (incl. collaborative delineation), single-slice, cross-slice and cross-scale query, integration at various levels… • Mapping the workflows to infrastructure • Registration (3d to 3d; 2d to 3d; based on coordinates; taxonomy (w/BIRNLex), a combination; cross-scale, etc.); image registration workflow; gene expression registration • Visualization: MBAT/WOMBAT • Integration: Interop API, mediator

  2. NeuroTerrain (Drexel) SMART Atlas (UCSD) SHIVA (UCLA) MBAT (BIRN) Mouse BIRN: Brain Image Analysis Systems BIRN Atlas Interoperability API

  3. 3D Anatomical Analysis Software • The Harvard SPL Anatomy Browser / 3D Slicerhttp://splweb.bwh.harvard.edu:8000/pages/papers/AnatomyBrowser/current/http://www.slicer.org/ • BRAINS2/IPL (The University of Iowa - another BIRN participant)http://www.psychiatry.uiowa.edu/wiki/index.php?title=Main_Page • The Pitt Supercomp. Center Volume Browser (Wetzel et al.)http://www.psc.edu/biomed/research/VB/ • Mouse Brain Image Visualizer (MBIV) (Bennett et al. - used for Hof atlas)http://vis7.bnl.gov/MouseAtlas/Visualization/main.html • 3DViewnixhttp://mipgsun.mipg.upenn.edu/~Vnews/ • ANFI (X11+Motif based medical imaging environment - including a volume browser)http://afni.nimh.nih.gov/afni/ • AMIDE (Gnome-based anatomical volume browser)http://amide.sourceforge.net/ • Mayo Clinic's ANALYZEhttp://www.mayo.edu/bir/Software/Analyze/Analyze1NEW.html • BLOX (JHU)http://sourceforge.net/projects/blox/ • BrainImageJava (Stanford Psych. Neuroimaging Lab)http://spnl.stanford.edu/tools/bijhilites.htm • BrainMaps.org (UC Davis - though really 2D, it should be considered capable of interoperating in 3D the way SMART Atlas does - even it cannot do this now)http://brainmaps.org/ • BrainVoyager QX (Rainer Goebel et al. atﾊBrain Innovation B.V., Maastricht, The Netherlands)http://www.brainvoyager.de/ • Brede (Finn 〉up Nielsen -ﾊIMM, Tech. U. of Denmark - XML-based from the outset)http://hendrix.imm.dtu.dk/software/brede/ • CARET/SumsDB (David van Essen, John Harwell, et al. - Wash. U. St. Louis)http://brainvis.wustl.edu/caret/ • NCMIR 3D Visualization Toolshttp://ncmir.ucsd.edu/Downloads/Software/overview.htm • XANAT/Conexus/Large-Scale Viz (UCDavis/Stanford Psych/UCI)http://redwood.ucdavis.edu/bruno/xanat/http://www.ece.uci.edu/~jmeyer/lsv.htmlhttp://nir.cs.ucdavis.edu/tools.jsp • FMRIDC Tool (Dartmouth)http://www.fmridc.org/f/fmridc/dmt.html?id=CAJfZRaA • DPTools (Denis Ducreux - France)http://193.55.58.11/DPTools/DPTools.htm • EM3D (U.J. McMahan - Stanford Neurobiology)http://em3d.stanford.edu • /Imaris (Bitplane AG)http://www.bitplane.com/products/imaris/imaris_product.shtml • Amira (Mercury Computer Systems)http://www.amiravis.com • /FormZ (auto-des-sys)http://www.formz.com/products/formz.html • itk-SNAP (currently - Penn Image Computing & Science Lag, Radiology, U.Penn)http://www.itksnap.org/ • Java Image Viz (JIV - McGill U.)http://www.bic.mni.mcgill.ca/users/crisco/jiv/ • MIPAV (NIH)http://mipav.cit.nih.gov/ • MRI3DX (Aston U., Birmingham UK)http://www.aston.ac.uk/lhs/staff/singhkd/mri3dX/mri3dX.jsp • MRIView (Los Alamos NL)http://www.lanl.gov/p/p21/mriview.shtml • NeuroLens (MGH Martinos Imaging Center)http://www.neurolens.org/ • NMV (Neuromorphometrics, Inc. - somewhat SMART Atlas-like)http://neuromorphometrics.org:8080/nvm/index.html • OsiriX - http://homepage.mac.com/rossetantoine/osirix/Index2.html • Skandha4/Brain Visualizer (U. Washington, Structural Informatics Group)http://quad.biostr.washington.edu/~andrew/cgi-bin/Brain_Browser.cgi?patient=P54 • SPM5 (UCL,ﾊWellcome Department of Imaging Neuroscience - U )http://www.fil.ion.ucl.ac.uk/spm/doc/theses/john/))http://www.fil.ion.ucl.ac.uk/spm/software/spm5/ • SurfRelax (NYU)http://www.cns.nyu.edu/~jonas/software.html • Volume One (VOLUME-ONE developers group, Japan - OpenGL/gtk+)http://www.volume-one.org/ • VoxBo (U. Penn.)http://www.voxbo.org/index.html • VTK CISG Registration Toolkit (Thomas Hartkens,ﾊGuy's Hospital, UC London - )http://www.image-registration.com/ • Volume Visualization and Navigation Toolhttp://www.medimagingsolutions.com/Services.htm • WFU PickAtlas (Wake Forest U., ANSIR resource)http://www.fmri.wfubmc.edu/download.htm

  4. Web-oriented Mouse BIRN Atlasing Tool (WoMBAT) • BIRN Atlas Interoperability API Promotes Re-use & Integration Messaging to synchronize & share • atlas data set selection • current atlas position • VOIs - object geometry & ontology-based labels • integrated analysis of brain section data sets aligned to any given atlas Messaging implementation • generators & listeners • process monitoring and control • WSDL web-services + binary attachments

  5. NeuroTerrain Atlasing System • 2005/2006 Progress Report NT Atlas Server • Re-architected as ANSI C/C++ Unix daemon app • Integrates Macrovoxel atlas data sets with brain region VOIs in a unified coordinate space • Responds to client slice requests via TCP socket-based data stream • Tuned for optimal performance under low & high network latency (local LAN vs. public Internet) • Tools for building Macrovoxel data sets

  6. NeuroTerrain Atlasing System • 2006/2007 Plans NT Atlas Server • Integrated, seamless zooming of aligned multi-dimensional data sets • Tools to integrate user-submitted brain segmentation • Implementation of the BIRN Atlas Interoperability API • Dedicated NT Server (dual 2GHz XNode) at BIRN-CC • Tools for tighter integration of VOI definitions with BIRNLex • Web service-based access to NT atlas aligned datasets (e.g., the Mouse Brain Library, etc.)

  7. NeuroTerrain Atlasing System • 2005/2006 Progress Report NetOStat Client (NT-SDK) • Re-architected as a Java-based dev kit components for integration in any Java application - client or server • NetOStat application serves as developer template • Provides complete implementation of the NT Server API • Select data set, slice data at arbitrary angles, switch slice axis (C/H/S), zoom & pan, view selected VOIs, save images, reslice for segmentation • Tuned for optimal performance under low & high network latency (local LAN vs. public Internet)

  8. From Mac only To platform independent Java NeuroTerrain Atlasing System NetOStat Client (NT-SDK)

  9. NeuroTerrain Atlasing System • 2006/2007 Plans NetOStat Client (NT-SDK) • Complete bi-directional implementation of BIRN Atlas Interoperability API in NT-SDK • Complete simultaneous, multi-session capability • Complete multiplatform testing - Windows, Linux, & Webstart • Continue network tuning • Web-service client to SRB & Mediator • Link with NT Image Repository server - deliver NT-aligned data sets to any implementing application

  10. Recent Additions to MBAT (UCLA) • Bonfire Browser • Query Bonfire server, display results • Improved Brain Graph Editing and Display • Integrated Gene Expression Tool • Query/display individual user data on BIRN • uArray Server • GeneNetwork • BIRN CC Mediator (Barlow/Zapala data)

  11. MBAT – Future Plans (UCLA) • Expand annotation searching for gene expression • Query/Display in-situ images • Add 2d <-> 3d interface with NeuroTerrain Server and Smart Atlas

  12. In the last 6 months (UCSD) • Closed the loop on image registration • Image registration workflow on the portal • Spatial registry in Oracle Spatial, with WS API • Load an image into Jibber – define registration points and compute transformation matrix – warp with Jetsam – serve the warped image as ArcIMS service – update record in spatial registry (including SDO, thumbnails, etc.) – discover the image by querying from Smart Atlas • Components implemented as web services, callable from other apps • The Bonfire module in SA and MBAT

  13. Image Registration Workflow • Step 1: Select an image in SRB, and start warping with Jibber

  14. Step 2: After warping is done, spatial registry is updated to reflect it; warped images are listed … … select a warped image for conversion to image service

  15. Step 3: Review image metadata … and spatial metadata in spatial registry

  16. Step 4: Find the image in spatial registry … … by specifying a search shape in Smart Atlas

  17. Development Ideas (UCSD) • Registering more images in the spatial registry, testing, validation… • Tools for data curation in spatial registry • Registering 3D volumes in a similar fashion • Integrating 3d cutting tools • Registering oblique slices • Web services and workflows for registering other data types, modeled after image registration • Wrapping spatial selection requests as Web services • Atlas interoperability API and server: connection with mediator API • Portalizing atlas functionality • BIRN-enabled tools (plugins for Photoshop, Excel, to allow upload/search/download from BIRN – need a survey of popular tools?) • Exchanging relative location information, for cross-scale communication • Better organization of ArcIMS image services, and serving images in OGC-compatible formats • Using ERMapper IWS or ESRI's Image server to serve large BIRN images into Photoshop and web clients

  18. Define a selection polygon in MBAT (2D or 3D) BIRN Tools Find by Location Find by Taxonomies Upload and Register Open an attribute selection form, w/Bonfire etc. Authenticate and start image registration workflow

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