INCF at SfN 2013: Daniel Wójcik presents open source web-based infrastructure (SBA, 3dBAR)
Channel: INCF
Date: 04/12/2013

Computer demo at SfN 2013, San Diego.
Presenter: Daniel Wójcik, Nencki Institute of Experimental Biology, Laboratory of Neuroinformatics, Poland
Title: Open source web-based infrastructure for brain atlas reconstruction, visualization
and mining: 3D Brain Atlas Reconstructor, Scalable Brain Atlas and a new marmoset brain template

Abstract:
One of the challenges of modern neuroscience is to integrate volumetric data of different modalities coming from different specimens. To foster these goals we need appropriate tools and reference data in the form of brain templates.

The Scalable Brain Atlas (SBA, scalablebrainatlas.incf.org) and the 3D Brain Atlas Reconstructor service (3dBARs, 3dbars.org) form an infrastructure for working with three-dimensional brain atlases which is species- and data agnostic. We have used this infrastructure to process several widely used atlases of mouse, rat, macaque and
human. We have recently included the first template of marmoset monkey cortex.

The open-source 3dBAR software facilitates creation of 3D brain atlases from two dimensional atlas data of different quality, complexity and origin using a Common Atlas Format (CAF) representation as an intermediate step to simplify processing and interoperability with other software. 3dBAR generates complete 3D models of desired structures in different formats. Most of its common functionality is implemented in the 3dBARs web service (including customizable reconstructions, downloads in various formats, and live view of 3D structures). It is available directly or through a plugin in the SBA allowing three dimensional visualization of brain regions. 

The SBA is a web-based, open-source interactive brain atlas, supporting a growing number of freely accessible brain parcellations (atlases, maps) for various species. Brain regions can be selected to launch queries to other web-based resources or websites can use the SBA to visualize sets of brain regions. SBA functionality can be extended with plugins through which external applications can interact with the SBA bidirectionally, such as the CoCoMac (Macaque macro connectivity) plugin, or the 3dBAR connection.

Mapping the cerebral cortex is a critical step in understanding the function of the human brain. Non-human primates can provide us with detailed information to help us understand the general organisation principles of the cerebral cortex. To a collection of brain templates from macaque, rhesus, human, rat and mouse we have added a parcellation of the cortex of the marmoset monkey, a promising primate animal model, obtained using a variety of techniques and consolidated into a standardized digital atlas. The data are available through the 3dBAR and SBA interfaces.

The 3dBAR project is co-financed by the European Regional Development Fund under the Operational Programme Innovative Economy, grant POIG.02.03.00-00-003/09. SBA development is co-funded by the INCF, the CoCoMac plugin by the German INCF Node (BMBF grant 01GQ0801), Helmholtz Association HASB and portfolio theme SMHB, JUGENE Grant JINB33, and EU Grant 269921 (BrainScaleS). This project is conducted within the INCF Programs on Ontologies of Neural Structures and Digital Brain Atlasing.