INCF Digital Atlasing Infrastructure (DAI): Managing Interoperable Atlas Spaces

Ilya Zaslavsky1, Jyl Boline2, Albert Burger3, Lydia Ng4 and Fons Verbeek5 1Univ. of California at San Diego, San Diego, CA, USA; 2Informed Minds, Wilton Manors, FL, USA; 3Human Genetics Unit, MRC, Edinburgh, UK ;

4Allen Inst. for Brain Science, Seattle, WA, USA; 5Leiden Inst. of Adv. Comp. Science, Leiden, The Netherlands

The vision of INCF-DAIThe INCF Digital Brain Atlas Program seeks to build a community infrastructurefor sharing growing volumes of multidimensional data of the rodent brain,making such data easy to publish, discover and access by researchers anywhere in the world.

Creating a canonical spatial and semanticframework, and standards for data exchange, are the critical first steps in making atlas data interoperable.

The INCF-DAI team

Atlas hubs and services

The central role of Waxholm Space

INCF-DAI componentsINCF-DAI is envisioned as a collection of distributed services that support publication, discovery and invocation of heterogeneous atlas resources. It will establish common access mechanisms for resources of different type (2D images, 3D volumes, cell models, gene expression data, surfaces, connectivity, etc.), and provide and govern respective standard API development, to ensure interoperability within the system.

Components of INCF-DAI service oriented architecture include:• formal models of atlas spaces and

coordinate systems• common ontologies• spatial and semantic registries• coordinate translation services• semantic translation services• standard services API for

discovering and accessing atlas data of different types

• methods of publishing atlas data as services

• standard client applications• data type-specific wrappers

Using the systemFrom a 3D Atlas Integration Client, a user can query registered atlases spatially. A probe can be placed in the 3D space of the viewer; coordinates of the probe are then determined and translated into other coordinate spaces as needed. In this way, the user can identify a POI and a) explore several gene expression databases (e.g. AGEA, EMAGE) for genes expressed at this location, b) retrieve additional images from registered atlases based on the POI location (e.g. from AGEA, UCSD), c) examine features segmented at POI in other atlases, and d) perform other queries supported by the services. For most of such requests, spatial transformations and feature label lookups are performed automatically via atlas service chains.

Digital Atlasing Task Force

ABA Service WHS Service UCSD Service EMAGE Service

Core Services

GetCapabilities, DescribeProcess

GetCapabilities, DescribeProcess

GetCapabilities, DescribeProcess

GetCapabilities, DescribeProcess

Known coordinate spaces

ABAvoxel, AGEA, ABAreference

WHS Paxinos EMAP

Lookup GetStructureNameByPOI

GetStructureNameByPOI

GetStructureNameByPOI

GetStructureNameByPOI

Coordinate translations

WHS AGEA,ABAreference ABAvoxel,AGEA ABAvoxel

Paxinos WHS EMAP WHS

Other, based on POI

Get2DImageAtPOI, GetCorrelationMap, GetGenesByPOI

Get2DImageAtPOI Get2DImageAtPOI, GetGenesByPOI

Based on structure

GetGenesByStructure GetGenesByStructure

The 3D atlas integration client

Coordinate systems used in neuroscience are often based on a set of landmarks, may be represented in one or more reference spaces expressed as 3D volumes, sets of reference plates, surfaces, etc. They may also have different origin, units, coordinate axes, may or may not be segmented, etc.

INCF-DAI attempts to describe them formally, and define spatial transformations between them.

Atlas resources at each INCF-DAI hub are exposed as standard web services. These services are registered at the INCF Central server, which can harvest additional metadata from each service.

The services can be (a) wrappers of existing services or web sites of a hub, ensuring that the functions can be invoked in a standard way, and (b) centrally-deployed functions that assist with spatial and semantic translations, and describe service capabilities.

This table lists services currently deployed for INCF-DAI hubs. Each service contains core methods which describe service capabilities, and supports one or more reference spaces and coordinate translation between these spaces and WHS. Most atlas services also support anatomic structure lookup methods and image retrieval. (As of August 2009; planned services in italic)

AGEA response to GetCorrelationMapByPOI

GetGenesByPOI returns gene information from

AGEA

Get2DImageByPOIreturns relatedimages from UCSD hub

Get2DImageByPOIreturns images from AGEA

Spatial transformations enable positioning a point of interest (POI) at approximately the same location in different atlases, to enable local spatial queries. INCF-DAI hubs host transformations between WHS and local coordinate spaces, expressed as web

services. The transformation services are registered at INCF Central.

Paxinos to WHS

(1.0,4.3,1.78)

(308,642,224)

WHS toAGEA,

ABAvoxel(AGEA:3825,5650,4650)

ABAvoxel to ABAreference

(1.19,5.13,1.70)

GetGenesByStructureNamereturns gene information

from EMAGE

data. It makes data registered to one spatial framework and coordinate system, available for spatial query and retrieval from any other spatial framework, provided that it has a WHS mapping.

INCF Central: Registry of Atlas Spaces

Waxholm Space (WHS) is developed as a canonical atlas space, to which other key reference atlases can be mapped. It is a centerpiece of spatial integration for atlas

INCF Digital Atlasing Task ForceLead: Mike Hawrylycz, Allen Institute for Brain Science, USA Program Coordinator: Jyl Boline, Informed Minds, USAMembers:

Albert Burger, Human Genetics Unit, MRC, UKPablo Burstein, Drexel University, USAChristian Haselgrove, University of Massachusetts, USANoritaka Ichinohe, RIKEN Brain Science Institute, JapanG. Allan Johnson, Duke University, USA Stephen Larson, University of California at San Diego, USAMaryann Martone, University of California at San Diego, USA Lydia Ng, Allen Institute for Brain Science, USA Jonathan Nissanov, Drexel University, USALuis Puelles, University of Murcia, Spain Seth Ruffins, University of California at Los Angeles, USA Fons Verbeek, Leiden University, The Netherlands Ilya Zaslavsky, University of California at San Diego, USA

Web site: http://www.incf.org/about/programs/atlasing

DevelopersNeuroscience scenarios: Maryann Martone, Stephen Larson (UCSD), Jyl

Boline (Informed Minds), Lydia Ng and Mike Hawrylycz (Allen Institute), Al Johnson (Duke University)

WHS dataset: Al Johnson and Jeff Brandenburg (Duke University), Jonathan Nissanov and Pablo Burstein (Drexel University)

Other datasets and meshes: Maryann Martone and Stephen Larson (UCSD), Lydia Ng and Chris Lau (Allen Institute)

INCF Central and atlas service wrappers: Asif Memon (UCSD)INCF hubs and local services: Lydia Ng (Allen Institute), Albert Burger

(MRC, UK), Kenneth McLeod (Heriot-Watt Univ, UK), Asif Memon (UCSD)Spatial transformations and anatomic structure lookup: Lydia Ng (Allen

Institute), Steven Lamont and Alexander Young (UCSD)Representation of coordinate spaces: Alexander Young (UCSD)Client development: Stephen Larson and UCSD team; Seth Ruffins and

UCLA teamHardware and server setup: Larry Lui (UCSD)Development lead: Ilya Zaslavsky (UCSD)