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

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.

Association of Caspase 3 Activation and H2AX γ Phosphorylation in the Aging Brain: Studies on Untreated and Irradiated Mice

“…As we have previously shown that γH2AX immunoreactive nuclei were widely distributed in numerous cortical areas including the primary and second auditory, motor, somatosensory and visual cortices—see Figure 1 in [ 13 ]—we were not interested in exploring differences among cortical areas in more depth. Also, our assessments in the hippocampus are consistent with the literature (Table 3 from [ 76 ], and data from the Allen Brain Atlas [ 77 ]). We found no literature data on the volumetric density of SVZ/RMS/OB cells that could be useful to compare with our current estimation.…”

“…Also, our assessments in the hippocampus are consistent with the literature (Table 3 from [76], and data from the Allen Brain Atlas [77]).…”

Connectivity characterization of the mouse basolateral amygdalar complex

“…Further, BLA.am cell bodies are 20% taller, 30% wider, and more spherical than BLA.ac neurons. While these differences are unlikely to affect computational functions, they could be useful features for future automated high-throughput cell identification 33 .…”

Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain

“…To further improve our ilastik segmentations, we implemented a post-processing step for the manual removal of erroneously segmented objects. To convert profile counts into cell number estimates for entire regions, it is necessary to address several sources of bias ( Attili et al., 2019 ). First, when the brain is cut into sections, some cells are split and can therefore appear in more than one section, which may lead to overcounting.…”