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INCF Digital Atlasing Infrastructure: Managing Interoperable Atlas Spaces

Ilya Zaslavsky1*, Jyl Boline2, Albert Burger3 and Fons Verbeek4
  • 1 University of California, San Diego, United States
  • 2 Informed Minds, United States
  • 3 MRC, Human Genetics Unit, United Kingdom
  • 4 Leiden Inst of Advanced Computer Science, Netherlands

The goal of the INCF Digital Atlasing task force is to define a common framework for exchanging information across neuroscience atlases (Digital Atlasing and Standardization in the Rodent Brain, Boline et al). This framework will encourage international sharing of brain data such as images, segmentations, annotations, gene expression, connectivity, electrophysiology and developmental data across scale, modality, and semantic and spatial frameworks. The INCF digital atlasing infrastructure (INCF-DAI) is envisioned as a collection of standard APIs and distributed services that support publication, discovery and invocation of heterogeneous atlas resources. The initial phase of INCF-DAI focuses on interoperability of mouse brain atlases, specifically on different ways of referencing spatial locations in the brain as a way to bridge different atlas spaces.

Multiple renditions of mouse brain space exist, including spatial referencing adopted in the Paxinos and Watson Atlas, Allen Brain Atlas (voxel and 2D reference plates), and the emerging Waxholm Space (WHS), currently being developed under the aegis of INCF (Waxholm Space: Target Volumes for A Standard Coordinate System for the Mouse Brain, Johnson et al). There exist many additional representations of space by other atlasing efforts, typically with image-based or ad hoc coordinate referencing. INCF-DAI seeks to make these representations of space interoperable, by:
1) formally describing the available spaces
2) defining transformations between WHS and other atlas spaces
3) developing a standard vocabulary/ontology for neural structures (this will be carried out as part of the INCF Program on Ontologies of Neural Structure, or PONs)
4) developing APIs for exchanging spatial information in WHS
5) creating a collection of brain space wrappers for translating requests formulated in WHS into native atlas space, and translating local data into WHS for visualization and integration
6) defining a procedure for registering additional atlas spaces to the common framework
7) supporting distributed querying of multiple WHS-compatible atlas databases

Once WHS-based coordinates become the standard in describing brain locations within this framework, WHS-aware tools, applications and integration resources can be constructed. The key components of the WHS-aware infrastructure include: 1) a database of atlas spaces containing metadata associated with each collection of reference images or volumes with segmented features and a defined coordinate system, as well as transformations between WHS and each of the spaces , 2) a resource registry containing metadata about various local atlas resources mapped to one of the available atlas spaces, 3) a spatial registration workflow that assists registration of their resources to a recognized atlas space and adding this information to the INCF-DAI framework, and 4) a distributed query service for WHS-compatible datasets.

When exposed via data discovery and retrieval service APIs, these components shall enable users to query atlas data by coordinates regardless of which space the data are registered to or the coordinate system adopted by the client application.
The development of the INCF-DAI is a community effort and all interested parties are encouraged to provide input and feedback.
For further details, contact Jyl Boline (jylboline@informedminds.info).

Conference: Neuroinformatics 2009, Pilsen, Czechia, 6 Sep - 8 Sep, 2009.

Presentation Type: Oral Presentation

Topic: Digital atlasing

Citation: Zaslavsky I, Boline J, Burger A and Verbeek F (2019). INCF Digital Atlasing Infrastructure: Managing Interoperable Atlas Spaces. Front. Neuroinform. Conference Abstract: Neuroinformatics 2009. doi: 10.3389/conf.neuro.11.2009.08.010

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Received: 21 May 2009; Published Online: 09 May 2019.

* Correspondence: Ilya Zaslavsky, University of California, San Diego, San Diego, United States, zaslavsk@sdsc.edu