For example, while it is possible to find reported cell and neuron numbers for larger cortical regions such as visual, somatosensory, or auditory areas ( Herculano-Houzel et al., 2013), the cellular content of their subdivisions into smaller functional areas or even layers remains unknown. One reason for this paucity of data is that most cell counting studies focus on large regions without examining their subdivisions (Figure 1B). Counts of glia, or the ratio of glia to neurons, are even less common and counts of neurons and glia belonging to specific types are still to be established (Figure 1B). Despite these efforts, neuron counts cover only about 4% of the hierarchical regions defined in the Allen Brain Atlas ( Lein et al., 2007 Dong, 2008). Since the seminal work of Ramon y Cajal over a century ago, a vast number of studies have used a wide range of methods to count stained cells in the brain. The atlas also provides insights into cellular organization only possible at this whole brain scale, and is publicly available. 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 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 AMBA. 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. In fact, neuron numbers are only available for about 4% of brain of regions and estimates often vary by as much as 3-fold. Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerlandĭespite vast numbers of studies of stained cells in the mouse brain, no current brain atlas provides region-by-region neuron counts.Csaba Erö *, Marc-Oliver Gewaltig †, Daniel Keller and Henry Markram
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