Atlas of Inhibitory Neurons in the Mouse Brain

The mouse brain contains a rich diversity of inhibitory interneuron types that have been characterized by their patterns of gene expression. However, the distribution of these cell types across the mouse brain is still incomplete. We developed a computational method to establish a consensus on the estimate of the densities of different interneuron types across the mouse brain. This method allows the unbiased integration of diverse and disparate datasets into a framework to predict interneuron densities for uncharted brain regions. We constrained our estimates based on previously computed brain-wide neuron density data, gene expression from in situ hybridization image stacks together with a wide range of values reported in the literature. Using optimization, we derived coherent estimates of cell densities for the different interneuron types. We estimated that 20.3% of all neurons in the mouse brain are inhibitory. Among all inhibitory neurons, 18% predominantly express parvalbumin (PV), 16% express somatostatin (SST), 3% express vasoactive intestinal peptide (VIP), and the remainder 63% belong to the residual GABAergic population. Our pipeline is extensible, allowing new cell types or data to be integrated as they become available. The data, algorithms, software, and results of this pipeline are publicly available and update the Blue Brain Cell Atlas. We find that our density estimations improve as more literature values are integrated. This work therefore leverages the research community to collectively converge on the numbers of each cell type in each brain region.