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 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… - PowerPoint PPT Presentation
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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
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
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/
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
• 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
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