integrating digital atlases of the brain: atlas services with wps ilya zaslavsky san diego...
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Integrating digital atlases of the brain: atlas services
with WPS
Ilya ZaslavskySan Diego Supercomputer Center, UCSD
Lead of the INCFDigital Atlasing Infrastructure Task Force
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What is an atlas?• A collection of 2D images or a 3D
volume, possibly with anatomic feature delineations and a set of additional annotations
What we need is more than an atlas:
– A gateway to large distributed databases of images, volumes, segmentations, gene expression data, electrophysiology, behavioral, connectivity, other spatially-registered data
• Ability to ask questions such as “which atlases have images for this part of the brain”, “what genes are expressed here in atlas A”, “compare spatial patterns of protein distribution across atlases”, etc.
– Collection of atlases organized as spatial data sources– Collection of spatial data registries, service APIs and workflows:
• image registration, segmentation, spatial selection, spatial analysis, integration of spatial data
– Collection of viewers, integration and annotation tools
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InternationalNeuroinformaticsCoordinatingFacility
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Purpose of this INCF program: To enhance the interoperability, accessibility, and sharing of spatial data sets in neuroscience: INCF-sponsored standards
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The Integration Problem: Whose standard?
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• INCF may play similar role to EPSG
• ListSRSs and DescribeSRS requests
• Published by atlas hubs
Spatial reference systems and SRS registry
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left
rightanterior
posterior
dorsal
ventral
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The Central Role of Waxholm Space
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Different types of transformations• ABAvoxel to WHS
– Large volumes for transforms in both directions, between 3D and 3D of different dimensions– Then simple lookup in the transformation volume
• ABAvoxel to ABAreference– Collection of conversion formulas for individual slices
• ABAvoxel to AGEA– Simple scaling
• WHS to Paxinos Mouse Atlas– Warping appropriate WHS cuts to match with Paxinos slices; translations per slice and brain
region
ListTransformationsGetTransformationChainDescribeTransformationTransformPOI
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Testing transformation chains: from Paxinos Reference Plates to ABA Reference Plates via WHS and AGEA/ABA
Initial point: (1.0, 4.3, 1.78)
Anterior to Bregma at 1.78 mm, Fig. 16
Structure= AC (anterior commissure)
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Testing, Step 1: Paxinos to WHS
The original
Transform to WHS using transformation service we built:http://incf-dev-local.crbs.ucsd.edu/ucsd/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=TransformPOI&DataInputs=transformationCode=Mouse_Paxinos_1.0_To_Mouse_WHS_0.9_v1.0;x=1;y=4.3;z=1.78
Result = 308,642,224
WHS coronal cut WHS coronal cut fitted with Paxinos plate
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Testing, Step 2: WHS to AGEA
The original
Transform to AGEA using Steve’s lookup over Lydia’s conversion matrix, wrapped in Asif’s service:http://incf-dev-local.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=TransformPOI&DataInputs=transformationCode=Mouse_WHS_0.9_To_Mouse_AGEA_1.0_v1.0;x=1;y=112;z=162
Result: 3825,5650,4650
WHS views
Looking at the result in AGEA:
http://mouse.brain-map.org/agea/all_coronal?correlation&seedPoint=3825,5650,4650
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Testing, Step 2: WHS to AGEA;Results in AGEA
The original
http://mouse.brain-map.org/agea/all_coronal?correlation&seedPoint=3825,5650,4650
Wrapped in GetCorrelationMap service: http://incf-dev-local.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=GetCorrelationMapByPOI&DataInputs=srsName=Mouse_AGEA_1.0;x=3825;y=5650;z=4650;filter=maptype:coronal
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Testing, Steps 3 and 4: AGEA to ABA volume to ABA reference plates
The original
Transform to ABA (i.e. divide by 25):http://incf-dev-local.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=TransformPOI&DataInputs=transformationCode=Mouse_AGEA_0.9_To_Mouse_ABAvoxel_1.0_v1.0;x=3825;y=5650;z=4650
Result: 153,226,186
Transform to ABA reference plate coordinates:http://incf-dev-local.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=TransformPOI&DataInputs=transformationCode=Mouse_ABAvoxel_0.9_To_Mouse_ABAreference_1.0_v1.0;x=3825;y=5650;z=4650
Result: 1.194, 5.127,1.693
Check the result in ABA reference atlas at http://mouse.brain-map.org/atlas/ARA/Coronal/browser.html(see http://mouse.brain-map.org/viewImage.do?imageId=130973 ) – we are in Coronal level 38, as predicted!
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The results, againThe original Paxinos
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Standardization of atlas servicesThe services use OGC Web Processing Service (WPS)
Waxholm Markup Language (WaxML):
XML schema that provides standard constructs for atlas services
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INCF hubs and INCF central
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Accessing atlases from the Whole Brain Catalog
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Demo
WHS web viewer
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The power of spatial integration frameworks
• Learning from geospatial infrastructure– Standard schemas and service interfaces for spatial data tuned to neuroscience
data– Borrowed some components of spatial data infrastructure
• Standards and services are being built up by cooperating teams– Across international boundaries– Creating atmosphere of collaboration where there has mostly been competition
• Data challenges– Managing spatial and semantic heterogeneity; registration– Multiple types and modalities of data– Consistent description and derivation of spatial reference systems and
transformations; uncertainty measures
• Computational challenges– Processing and spatial registration of large images– Data mining across atlases– Synchronization between atlases
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Coding examples, schemas, guidelines
http://code.google.com/p/incf-dai/wiki/AtlasRequestInterfaceSpec
Soon: “hub building toolkit”
http://www.incf.org/WaxML/xmlschema
WaxML:
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Resources for developershttp://waxholm.neurocommons.org/page/Background_for_Developers
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