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

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/http://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_Pagehttp://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/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.htmlhttp://vis7.bnl.gov/MouseAtlas/Visualization/main.html 3DViewnixhttp://mipgsun.mipg.upenn.edu/~Vnews/http://mipgsun.mipg.upenn.edu/~Vnews/ ANFI (X11+Motif based medical imaging environment - including a volume browser)http://afni.nimh.nih.gov/afni/http://afni.nimh.nih.gov/afni/ AMIDE (Gnome-based anatomical volume browser)http://amide.sourceforge.net/http://amide.sourceforge.net Mayo Clinic's ANALYZEhttp://www.mayo.edu/bir/Software/Analyze/Analyze1NEW.htmlhttp://www.mayo.edu/bir/Software/Analyze/Analyze1NEW.html BLOX (JHU)http://sourceforge.net/projects/blox/http://sourceforge.net/projects/blox/ BrainImageJava (Stanford Psych. Neuroimaging Lab)http://spnl.stanford.edu/tools/bijhilites.htmhttp://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/http://brainmaps.org BrainVoyager QX (Rainer Goebel et al. at ﾊ Brain Innovation B.V., Maastricht, The Netherlands)http://www.brainvoyager.de/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/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/http://brainvis.wustl.edu/caret/ NCMIR 3D Visualization Toolshttp://ncmir.ucsd.edu/Downloads/Software/overview.htmhttp://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.jsphttp://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=CAJfZRaAhttp://www.fmridc.org/f/fmridc/dmt.html?id=CAJfZRaA DPTools (Denis Ducreux - France)http://193.55.58.11/DPTools/DPTools.htmhttp://193.55.58.11/DPTools/DPTools.htm EM3D (U.J. McMahan - Stanford Neurobiology)http://em3d.stanford.eduhttp://em3d.stanford.edu /Imaris (Bitplane AG)http://www.bitplane.com/products/imaris/imaris_product.shtmlhttp://www.bitplane.com/products/imaris/imaris_product.shtml Amira (Mercury Computer Systems)http://www.amiravis.comhttp://www.amiravis.com /FormZ (auto-des-sys)http://www.formz.com/products/formz.htmlhttp://www.formz.com/products/formz.html itk-SNAP (currently - Penn Image Computing & Science Lag, Radiology, U.Penn)http://www.itksnap.org/http://www.itksnap.org Java Image Viz (JIV - McGill U.)http://www.bic.mni.mcgill.ca/users/crisco/jiv/http://www.bic.mni.mcgill.ca/users/crisco/jiv/ MIPAV (NIH)http://mipav.cit.nih.gov/http://mipav.cit.nih.gov MRI3DX (Aston U., Birmingham UK)http://www.aston.ac.uk/lhs/staff/singhkd/mri3dX/mri3dX.jsphttp://www.aston.ac.uk/lhs/staff/singhkd/mri3dX/mri3dX.jsp MRIView (Los Alamos NL)http://www.lanl.gov/p/p21/mriview.shtmlhttp://www.lanl.gov/p/p21/mriview.shtml NeuroLens (MGH Martinos Imaging Center)http://www.neurolens.org/http://www.neurolens.org NMV (Neuromorphometrics, Inc. - somewhat SMART Atlas-like)http://neuromorphometrics.org:8080/nvm/index.htmlhttp://neuromorphometrics.org:8080/nvm/index.html OsiriX - http://homepage.mac.com/rossetantoine/osirix/Index2.htmlhttp://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=P54http://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/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.htmlhttp://www.cns.nyu.edu/~jonas/software.html Volume One (VOLUME-ONE developers group, Japan - OpenGL/gtk+)http://www.volume-one.org/http://www.volume-one.org VoxBo (U. Penn.)http://www.voxbo.org/index.htmlhttp://www.voxbo.org/index.html VTK CISG Registration Toolkit (Thomas Hartkens, ﾊ Guy's Hospital, UC London - )http://www.image-registration.com/http://www.image-registration.com Volume Visualization and Navigation Toolhttp://www.medimagingsolutions.com/Services.htmhttp://www.medimagingsolutions.com/Services.htm WFU PickAtlas (Wake Forest U., ANSIR resource)http://www.fmri.wfubmc.edu/download.htmhttp://www.fmri.wfubmc.edu/download.htm

4. Web-oriented Mouse BIRN Atlasing Tool (WoMBAT) BIRN Atlas Interoperability API 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 WSDL web-services + binary attachments process monitoring and control Promotes Re-use & Integration

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 for tighter integration of VOI definitions with BIRNLex Web service-based access to NT atlas aligned datasets (e.g., the Mouse Brain Library, etc.) Tools to integrate user-submitted brain segmentation Implementation of the BIRN Atlas Interoperability API Dedicated NT Server (dual 2GHz XNode) at BIRN-CC

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 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) NetOStat application serves as developer template

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

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

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

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