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Front. Neuroinform. | doi: 10.3389/fninf.2018.00084

A Cell Atlas for the Mouse Brain

  • 1Blue Brain Project, Ecole polytechnique fédérale de Lausanne (EPFL), Switzerland

Despite vast numbers of studies of stained cells in the mouse brain, no current brain atlas provides region-by-region neuron counts. In fact, neuron numbers are only available for about 4% of brain of regions and estimates often vary by as much as three-fold. Here we provide a first 3D cell atlas for the whole mouse brain, showing cell positions constructed algorithmically from whole brain Nissl and gene expression stains, and compared against values from the literature. The atlas provides the densities and positions of all excitatory and inhibitory neurons, astrocytes, oligodendrocytes and microglia in each of the 737 brain regions defined in the Allen Mouse Brain Atlas. The atlas is dynamic, allowing comparison with previously reported numbers, addition of cell types, and improvement of estimates as new data is integrated. The atlas also provides insights into cellular organization only possible at this whole brain scale, and is publicly available.

Keywords: cell numbers, Neurons, glia, mouse brain, Allen Brain Atlas

Received: 30 Aug 2018; Accepted: 25 Oct 2018.

Edited by:

Qingming Luo, Huazhong University of Science and Technology, China

Reviewed by:

Hong-Wei Dong, Laboratory of Neuro Imaging - University of Southern California, United States
Jingpeng Wu, Princeton University, United States  

Copyright: © 2018 Erö, Gewaltig, Keller and Markram. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Mr. Csaba Erö, Blue Brain Project, Ecole polytechnique fédérale de Lausanne (EPFL), Geneva, Switzerland,