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bioRxiv · 10.1101/635201

Cell numbers, distribution, shape, and regional variation throughout the murine hippocampal formation from the adult brain Allen Reference Atlas

Attili, S. M.·Silva, M.·Nguyen, T.-V.·Ascoli, G.
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Abstract

Quantifying the distribution of cells in every brain region is fundamental to attaining a comprehensive census of distinct neuronal and glial types. Until recently, estimating neuron numbers involved time-consuming procedures that were practically limited to stereological sampling. Progress in open-source image recognition software, growth in computing power, and unprecedented neuroinformatics developments now offer the potentially paradigm-shifting alternative of comprehensive cell-by-cell analysis in an entire brain region. The Allen Brain Atlas provides free digital access to complete series of raw Nissl-stained histological section images along with regional delineations. Automated cell segmentation of these data enables reliable and reproducible high-throughput quantification of regional variations in cell count, density, size, and shape at whole-system scale. While this strategy is directly applicable to any regions of the mouse brain, we first deploy it here on the closed-loop circuit of the hippocampal formation: the medial and lateral entorhinal cortices; dentate gyrus (DG); areas Cornu Ammonis 3 (CA3), CA2, and CA1; and dorsal and ventral subiculum. Using two independent image processing pipelines and the adult mouse reference atlas, we report the first cellular-level soma segmentation in every sub-region and layer of the left hippocampal formation through the full rostral-caudal extent, except for the (already well characterized) principal layers of CA and DG. The overall numbers ([~]600k cells in entorhinal cortex, [~]200k in DG, [~]430k in CA1-3, and [~]290k in subiculum) are corroborated by traditional stereological sampling on a data subset and well match sparse published reports.

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Attili, S. M., Silva, M., Nguyen, T.-V., Ascoli, G.. 2019-05-10. Cell numbers, distribution, shape, and regional variation throughout the murine hippocampal formation from the adult brain Allen Reference Atlas. https://doi.org/10.1101/635201

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