Mouse Brain Atlas Meeting

Use casese.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/WOMBATIntegration: Interop API, mediator

Mouse BIRN: Brain Image Analysis Systems

SMART Atlas (UCSD)

BIRN Atlas Interoperability API

MBAT (BIRN)

NeuroTerrain (Drexel)

SHIVA (UCLA)

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

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

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 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

NeuroTerrain Atlasing System

2005/2006 Progress ReportNetOStat 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

NeuroTerrain Atlasing System

NetOStat Client (NT-SDK)

FromMac only

To platform independent Java

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

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

… 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 …

• 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

Find by LocationFind by TaxonomiesUpload 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