Blue Brain Cell Atlas

The first digital 3D cell atlas of the whole mouse brain

The Blue Brain Cell Atlas is the first digital 3D cell atlas of the whole mouse brain. It provides neuroscientists with a unique insight into the cellular composition of the mouse brain. Users can view and download the number, major types and 3D positions of all neurons and glia in all 737 areas of the mouse brain.

The Blue Brain Cell Atlas provides the densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of the brain regions defined in the Allen Mouse Brain Atlas.

Blue Brain’s Cell Atlas was constructed by placing cells computed from whole brain Nissl and gene expression stains from the Allen Institute for Brain Science. Gene expression stains were used to decide the major type of cell. The API provided by the Allen Mouse Brain Atlas was used to access the data.

Cell numbers and tissue distributions were validated against values from the literature where available. We found that the literature only contains specific values for 4% of the 737 brain regions.

The atlas fills the gap of cell numbers for 96% of brain regions. Blue Brain found that experimental data cannot provide ground truth-values and therefore we developed a dynamic cell atlas that can integrate diverse datasets to converge towards ground truth-values, in principle for every cell-type in all brain regions.

More detailed classification of cell-types can therefore be included and estimates for these can be iteratively improved, as new data is integrated.The user can also submit region and cell type specific densities and numbers obtained in new experiments for comparison and, to help with the convergence towards the ground truth. New data will be used to further improve both the next iteration of the Cell Atlas and its validation.

Erö, C., Gewaltig, M.-O., Keller, D., and Markram, H. (2018). A Cell Atlas for the Mouse Brain. Frontiers in Neuroinformatics 12, 84.
DOI: 10.3389/fninf.2018.00084

Atlas Alignment – a toolbox from the Blue Brain that performs multi-modal image registration and alignment supports use of the Cell Atlas. It can be used to fix any misalignment between ISH stains and Nissl stains within the Blue Brain Cell Atlas. Find out more –