data sharing made easy

Get started

Install, segment cells and processes, register section to atlas, generate webatlas.

How to install

Get started by installing and compiling necessary third party libraries for using WholeBrain. Installation instructions currently available for: OSX. WholeBrain requires the installation of OpenCV and R the statistical package. For Bayesian statistical inference with WholeBrain we highly recommend STAN (mc-stan.org).


Depending on the signal-to-noise ratio of the fluorescent signal segmentation can either be done directly using only a set of binary thresholds and exclusion criterias, or by defining cell-bodies as occupying a specific spatial scale. With the later algorithm segmentation of labeled processes can also be achieved.


Registration is the process of finding a transform from an image of your brain section to that of a standardized reference atlas. The resulting output is both the coordinates of any segmented objects such as cells or processess within the reference atlas, as well as defining region boundaries in the original image.

Generate web-based maps

Share your sections or easily inspect the result manually from any JavaScript supporting browser. At the moment we recommend Firefox, Chrome or Safari, in that order. The web-based interface is especially designed to be used together with mobile devices, so called responsive design. see openbrainmap.org

What is WholeBrain?

WholeBrain is a Neuroanatomical Information System (NIS).
data on the fly

WholeBrain is a Neuroanatomical Information System (NIS) which means that it is a set of computerized information systems for the management and analysis of data that is spatially anchored within the mouse brain.

Neuroanatomical data obtained form miscroscope images is encoded and stored in stereotactic coordinate form, while external data such as behavioral output, or physiological recordings can be stored and managed using conventional spreadsheets. By linking table data to an object, region or location the stereotactic brain atlas, we can illustratively present different characteristics. This opens up opportunities for the analysis of spatial distributions, co-variations and geographical distributions.


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