1. Integrating digital atlases of the brain: atlas services with WPS Ilya Zaslavsky San Diego Supercomputer Center, UCSD Lead of the INCF Digital Atlasing Infrastructure Task Force

2. 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

3. International Neuroinformatics Coordinating Facility

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

5. The Integration Problem: Whose standard?

6. INCF may play similar role to EPSG ListSRSs and DescribeSRS requests Published by atlas hubs Spatial reference systems and SRS registry

7. left right anterior posterior dorsal ventral

8. The Central Role of Waxholm Space

9. 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 ListTransformations GetTransformationChain DescribeTransformation TransformPOI

10. 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)

11. 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

12. 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_AG EA_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

13. Testing, Step 2: WHS to AGEA; Results in AGEA The original http://mouse.brain- map.org/agea/all_coron al?correlation&seed Point=3825,5650,4650 Wrapped in GetCorrelationMap service: http://incf-dev- local.crbs.ucsd.edu/aba/atlas?se rvice=WPS&version=1.0.0&requ est=Execute&Identifier=GetCorr elationMapByPOI&DataInputs=s rsName=Mouse_AGEA_1.0;x=3 825;y=5650;z=4650;filter=mapty pe:coronal

14. 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_ABAreferen ce_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 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!http://mouse.brain-map.org/viewImage.do? imageId=130973

15. The results, again The original Paxinos

16. Standardization of atlas services The services use OGC Web Processing Service (WPS) Waxholm Markup Language (WaxML): XML schema that provides standard constructs for atlas services

17. INCF hubs and INCF central

18. Accessing atlases from the Whole Brain Catalog

19. Demo WHS web viewer

20. 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

21. Coding examples, schemas, guidelines http://code.google.co m/p/incf- dai/wiki/AtlasRequest InterfaceSpec Soon: “hub building toolkit” http://www.incf.org/ WaxML/xmlschema WaxML:

22. Resources for developers http://waxholm.neurocommons.org/page/Background_for_Developers