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Online repository of three-dimensional models of brain structures

Filed under:

Piotr Majka (Nencki Institute of Experimental Biology), Jakub M. Kowalski (Nencki Institute of Experimental Biology), Natalia Chlodzinska (Nencki Institute of Experimental Biology), Daniel K. Wójcik (Nencki Institute of Experimental Biology)

Brain atlases provide key reference frameworks for neuroscience. With the advancement of technology traditional 2D atlases are being complemented by digital 3D atlases, which are more flexible and better adapted to address modern computational, analytical and visualisation challenges of neuroscience.

Although the number of available brain atlases grows, the set of tools facilitating systematic access to these data is limited. To provide an easy access to a range of neuroanatomical data we created the 3D Brain Atlas Reconstructor web service ( – an on-line repository of brain atlases and 3D models of brain structures. The essential part of the 3dBAR service is a browser-based interface providing a wide range of functionalities including:

 - Browsing and downloading of reconstructed 3D models of brain structures in form of polygonal mesh or a volumetric dataset;
 - Previewing and manipulating the models within the browser window using WebGL technology, without necessity of installing additional software;
 - Accessing and downloading brain atlas packages consisting of a series of SVG slices or labelled NIfTI volumes;
 - Generation and management of custom reconstructions (e.g. processed with non-standard pipeline or generating result in an additional file format) using on-line reconstruction wizard.

Currently, there are several atlases available through the service, including various delineations of the INCF Waxholm Space mouse brain reference, Allen Brain Institute mouse reference atlas, and a collection of atlases distributed by the Scalable Brain Atlas project ( Some of them are intrinsically 3D atlases based on MRI scans while others are reconstructed from collections of 2D delineations. We can also host additional atlases.

Modern data repository should provide a convenient interface for data exchange and allow integration of its services with other systems or software. To facilitate interoperability with third-party applications we offer a complete application programming interface consisting of a set of HTTP queries providing the developers with programmatic access to resources we provide. Currently this mechanism is used by ScalableBrainAtlas, website and WaxML services developed by INCF DAI.

The project is supported by an infrastructural grant from the Polish Ministry of Regional Development POIG.02.03.00-00-003/09.
Preferred presentation format: Poster
Topic: Digital atlasing

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