Slide 1 - SDSC

							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
Mouse BIRN: Brain Image Analysis Systems




 NeuroTerrain (Drexel)                        SMART Atlas
                                                (UCSD)
                            SHIVA (UCLA)




                                               BIRN Atlas
                                           Interoperability API
              MBAT (BIRN)
  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
 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
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
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.)
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)
NeuroTerrain Atlasing System
NetOStat Client (NT-SDK)




   From
Mac only




              To platform independent Java
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
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)
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
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
                     Image
                   Registration
                    Workflow




• Step 1: Select
  an image in
  SRB, and start
  warping with
  Jibber
                    • 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
                    • Step 3:
                      Review image
                      metadata




… and spatial
 metadata in
 spatial registry
                    • Step 4: Find the
                      image in spatial
                      registry …




… by specifying a
 search shape in
 Smart Atlas
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
BIRN Tools                          Define a selection
                                   polygon in MBAT (2D
                                          or 3D)
             Find by Location
             Find by Taxonomies
             Upload and Register    Open an attribute
                                     selection form,
                                     w/Bonfire etc.



                                     Authenticate and
                                        start image
                                   registration workflow