Event Abstract

Scalable Brain Atlas: From Stereotaxic Coordinate to Delineated Brain Region

  • 1 Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, Netherlands
  • 2 University of California at San Diego, Department of Neurosciences, United States
  • 3 Friedrich-Alexander-University , Department of Pharmacology, Germany
  • 4 Nencki Institute of Experimental Biology, Poland

The Scalable Brain Atlas (SBA) is a web-based interactive brain atlas. It displays brain atlas templates (parcellations) for a variety of species and atlas providers. 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. The atlas templates are stored as a set of (preferably coronal) slices in Scalable Vector Graphics (SVG) format.

In support of the INCF Taskforce on Digital Atlasing Infrastructure (DAI), a number of services are built on top of the SBA. A user guide is available at http://scalablebrainatlas.incf.org/howto.

1] Thumbnail Service, which allows other websites to embed visual representations of a named brainsite in their code. This service is called as http://scalablebrainatlas.incf.org/thumbnail.php?Q, where Q contains parameters specifying brain atlas, structure name and appearance of the returned image. Internally, the service generates a quasi 3D representation of the brain region, and performs an SVG-to-PNG conversion using the GraphicsMagic php-module. An image cache is maintained to reduce server load. This service is extensively used by the NeuroLex Semantic Wiki pages at http://neurolex.org.

2] Coordinate to Brain Region service, which translates a stereotaxic coordinate to a named brain region. This service is called with parameters specifying the atlas space, and the X, Y and Z stereotaxic coordinates. It is implemented by first finding the slice nearest to coordinate X. The SVG image of this slice is converted to a color-coded PNG image. The Y,Z coordinate is then rescaled to a pixel value; the color value of this pixel provides the key to the brain region name. We plan to also support probabilistic brain atlases, returning a list of region names sorted by probability.

3] Atlas Template to Atlas Space Projection service, which projects an atlas template onto a non-native atlas space. 'Atlas template' refers to the segmentation of the brain in distinct regions, whereas an 'Atlas Space' represents the shape of an individual or averaged brain, typically derived from MRI data, CT scans and/or from stacks of histochemically prepared slices. This service relies on warping services provided by other hubs in the DAI framework. The warping can be guided by the gray/white matter contours, or by sets of fiducials: landmarks that are clearly distinguishable in both spaces. Two use cases are supported: (a) Display a stereotaxic coordinate from a non-native space on a chosen atlas space. For example, a Paxinos-Franklin mouse coordinate can be displayed in Waxholm space. This service finds the brain region at the warped coordinate, and opens the SBA with the brain region highlighted and the coordinate marked. (b) Display an entire template in non-native space. This service relies on precomputed template transformations. It can be combined with (a) to display a stereotaxic coordinate onto the warped template.

The SBA and its services are open source, and not species- or atlas specific. We actively search for new atlas templates to be imported into the SBA. The first and featured template is the Paxinos et al. Macaque atlas, manually traced by the Rolf Kötter group. In addition to this we are importing a number of Macaque parcellations provided by the David van Essen lab, using their Caret software, as well as the Martin-Bowden atlas. For the mouse, we have imported the Allen reference brain atlas from their application program interface, and we acquired an automatically labeled coarse partitioning of the Waxholm space. We are currently working with Sandra Strobelt and Andreas Hess to get the Paxinos and Franklin (2nd ed.) template into the SBA, based on manually redrawn polygons. Finally, the group of Daniel Wójcik is developing algorithms to replace the tedious process of manually creating polygons from scanned atlas templates by automated parsing of pdf/eps source files.

Conference: Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.

Presentation Type: Poster Presentation

Topic: Digital atlasing

Citation: Bakker R, Larson SD, Strobelt S, Hess A, Wòjcik D, Majka P and Kötter R (2010). Scalable Brain Atlas: From Stereotaxic Coordinate to Delineated Brain Region. Front. Neurosci. Conference Abstract: Neuroinformatics 2010 . doi: 10.3389/conf.fnins.2010.13.00028

Received: 02 Jun 2010; Published Online: 02 Jun 2010.

* Correspondence: Stephen D Larson, University of California at San Diego, Department of Neurosciences, La Jolla, United States, stephen.larson@gmail.com

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