Plugin architecture for the INCF Scalable Brain Atlas: CoCoMac and beyond

Rembrandt Bakker (Donders Institute, Radboud University Nijmegen), Markus Diesmann (Institute of Neuroscience and Medicine (INM-6), Research Center Jülich), Thomas Wachtler (Department Biology II, Ludwig-Maximilians-Universität München)

The Scalable Brain Atlas (SBA) [1] is a web-based, open-source interactive brain atlas, supporting a growing number of freely accessible brain parcellations (atlases, maps) for various species. We present a plugin architecture through which external applications can interact with the SBA bidirectionally, with the CoCoMac connectivity database as a prime example.

An external plugin consists of a JavaScript file with an ‘applyStateChange’ function which is called when a user selects a new brain region, slice, viewing angle or point of interest. Inside the applyStateChange function, the application can retrieve information from an external server using the json message protocol [2], and it can display the response in html layout or by placing stereotaxic coordinate markers in the 2-D and 3-D view panels of the SBA. The script may also define an ‘activate’ function, which is called before any user interaction.

An external plugin is activated by calling the SBA with an additional plugin parameter, which specifies the full URL to the JavaScript file. To get started, a documented example plugin is available. To see it in action inside the PHT00 monkey template, use If the plugin is targeted for public release, it can be developed and tested as an external plugin, to be later submitted to the SBA administrator as an internal, public plugin.

The CoCoMac [3] plugin is such an internal plugin which fully exploits SBA's capabilities. It is bidirectional: the SBA sends information about the selected brain region to the newly developed CoCoMac website at, which returns all outgoing axonal projections for that region. The SBA sorts the projections by estimated strength, and presents the results both in tabular form and as a set of stereotaxic markers, which are brighter for stronger connections. The table contains deep links back into the CoCoMac website, where the algorithm that computed the connection strength (tracer injections, nomenclature transformations) is made completely transparent. Direct link:

Another recently developed external plugin is the Brain Atlas Reconstructor ( plugin. It converts brain region contours from 2-D atlas plates into 3-D surface representations, which can then be downloaded or rendered in WebGL-capable browsers. Direct link:

The plugin architecture is also an excellent way to expose data harvested by the INCF Digital Atlasing Infrastructure (DAI) [4] to the user community. Already the DAI services are used to transform coordinates between various mouse atlas templates ( 

Funded by INCF (SBA development), German Neuroinformatics Node (hosting & development CoCoMac 2.0), and EU Grant 269921 (BrainScaleS), DIP F1.2, Helmholtz Alliance on Systems Biology (Germany), and Next-Generation Supercomputer Project of MEXT (Japan).


[1] R. Bakker et al. (2010), Front. Neurosci. Conference Abstract: Neuroinformatics 2010, doi: 10.3389/conf.fnins.2010.13.00028.

[2] Michael Mahemoff (2006), "Ajax Design Patterns", O'Reilly Media, ISBN 978-0-596-10180-0.

[3] Kötter R. (2004), Neuroinformatics. 2(2), pp. 127-44.

[4] Hawrylycz et al. (2011), PLoS Comput Biol 7[2]: e1001065. doi:10.1371/journal.pcbi.1001065.
Plugin architecture for the INCF Scalable Brain Atlas: CoCoMac and beyond
The CoCoMac plugin in action inside the Paxinos et. al. rhesus monkey atlas. The coordinate markers point to the approximate location of brain regions, their brightness indicates the strength of the axonal projection from the selected region to the marked region.
Preferred presentation format: Demo
Topic: Digital atlasing

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