Atlas Interoperability Session Ilya Zaslavsky, Willy Wong + Bill Bug + Heng Yuan

Why atlas integration Multiple atlases exist, to present different kinds of data, and offer different analysis and visualization functions Atlas authors are best to decide what presentation and functionality are most appropriate for their data Atlas authors tend to like their atlases more than other atlases –which creates a set of contradictory requirements… Needs: –Ability to search, query, retrieve different images, volumes, and segmentations, from any atlas of choice –Ability to easily switch between atlases

Interoperability desiderata Read data from other atlases/databases API for data retrieval and transformation Find relevant data in other atlases/ databases API for atlas catalogs View the region of interest in another atlas API for atlas state exchange MBAT Drexel’s NT UCLA’s Shiva Smart Atlas Gensat Allen Brain Atlas CCDB, others Spatial registry

Mechanisms of integration Directly: –By space, using Stereotaxic coordinates Formal coordinate system definitions Coordinate system translation services (incl. between image and stareotaxic) Spatial registration of images and segmentations –By anatomic feature names, via UMLS + Bonfire + Neuronames + BIRNLex… Ontological registration Semantic translation services Indirectly –By verbal description of spatial locations relative to well- defined features (rules) –In relative coordinates; by matching derived indices: histograms, shape indexes, etc.

Mechanisms of integration: 2  Integration across atlas clients Specification of state of atlas client API for initializing exchange service and submitting and retrieving states Servlet Or Web Service NT Shiva MBAT WOMBAT Smart Atlas Init() New service id & URL Open SmartAtlas using returned URL Submit() Confirmation Retrieve() Result wrapped in XML End_service() Confirmation Retrieve() Result wrapped in XML Submit() Confirmation Service ended automatically when application is closed

The current implementation

The message exchange WS er.jws?wsdlhttp:// :8080/axis/InterAtlasServ er.jws?wsdl –InitState –Submit_Ontology_Terms –Submit_stereotaxic_2D_pointlist –Submit_stereotaxic_3D_pointlist –Retrieve_Ontology_Terms –Retrieve_Stereotaxic_2D_Pointlist –Retrieve_Stereotaxic_3D_Pointlist –Clear_Ontology_Terms –Clear_Stereotaxic_All_Pointlist –Logout

Agreed-upon ROI description and state exchange protocol STATE_INIT:: user pwd STATE_SUBMIT smart m1,n1,p1 m2,n2,p2 x1,y1,z1 x2,y2,z2... m1,n1,p1 m2,n2,p2 x1,y1,z1 x2,y2,z2... success STATE_RETRIEVE shiva smart m1,n1,p1 m2,n2,p2 x1,y1,z1 x2,y2,z2... m1,n1,p1 m2,n2,p2 x1,y1,z1 x2,y2,z Java API

State Exchange between NT & SA We have a set of JAVA APIs for the external programmers to specify a Paxinos Plate (via Stereotaxic coordinates). We are still in the process of integrating NT/SA with the existing Interoperability Webservice APIs (2D exchange, tuning NT knife to available Paxinos for NT ->SA; the SA ->NT direction is straightforward)

State Exchange between SA-MBAT Atlas alignment problems… Transformation matrix wrapped in Coordinate Transformation Service

Exchanging atlas state in a format-independent manner Several formats for state: –pointlist3D, plane_pointlist2D, canonical_sagittal; plane_filling_pixels, plane_quadrtree, plane_bounding_pixels; filling_voxels, octtree, surface_bounding_voxels –Ontology-based + verbal state descriptions (?) Coordinate transformation services – sdlhttp:// :8080/axis/MouseCoordinate.jws?w sdl (Shiva to SmartAtals)

Universal description of location?? Should work across scales and coordinate systems, (eventually across species, development stages?) Location description: –By geometries (in common coordinates: there are three of them at least) –By feature names (in shared ontology) – Neuronames most likely –By relationships (in common mereotopology terms): need engines for “packing” and “unpacking” collections of mereotopological rules describing relative location of ROI w.r.t. common features –NEED TRANSLATIONS BETWEEN THE THREE

Atlas Interop API: thoughts MGI (they don’t do atlasing) and other collaborators Semantic web community interested in integration with spatial semantics UCSC site with more image data (VISIGENE) 6-month application timeframe –MRI +Protein localization +microarray, within a project; 2 other projects –Parkinsonian dataset as a use case - linkages to human Connectivity - USC, Hong Wei, COCOMAC Visualization integration – 2D into 3D Building (not) a Prius rather than two cars Making canonical anatomical presentations accessible 2D exchange definitely a short-term focus, but keep wider spectrum in mind Formal specifications of coordinate systems and describing existing datasets in these terms Develop more transformation routines, for the defined coord systems Pull more Gensat data into the atlasing environment? (start with data that we already have) Use cases for when you switch from one integration mdoe (bring data into your current interface) to inter-atlas API