Integrating digital atlases of the brain: atlas services

with WPS

Ilya ZaslavskySan Diego Supercomputer Center, UCSD

Lead of the INCFDigital Atlasing Infrastructure Task Force

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

InternationalNeuroinformaticsCoordinatingFacility

Purpose of this INCF program: To enhance the interoperability, accessibility, and sharing of spatial data sets in neuroscience: INCF-sponsored standards

The Integration Problem: Whose standard?

• INCF may play similar role to EPSG

• ListSRSs and DescribeSRS requests

• Published by atlas hubs

Spatial reference systems and SRS registry

left

rightanterior

posterior

dorsal

ventral

The Central Role of Waxholm Space

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

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)

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

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

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

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!

The results, againThe original Paxinos

Standardization of atlas servicesThe services use OGC Web Processing Service (WPS)

Waxholm Markup Language (WaxML):

XML schema that provides standard constructs for atlas services

INCF hubs and INCF central

Accessing atlases from the Whole Brain Catalog

Demo

WHS web viewer

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

Coding examples, schemas, guidelines

http://code.google.com/p/incf-dai/wiki/AtlasRequestInterfaceSpec

Soon: “hub building toolkit”

http://www.incf.org/WaxML/xmlschema

WaxML:

Resources for developershttp://waxholm.neurocommons.org/page/Background_for_Developers