In a project led by David Elkind, Master student with Noam Shental of OpenU, we made use of hundreds of full brains imaged by the Allen Mouse Brain Connectivity Atlas. The atlas used autofluorescence in the red channel for anatomic alignment– and we saw that cell nuclei lacked this autofluorescence. David trained a DNN to segment nuclei, and quantified cell densities, counts, and region volumes, for hundreds of mouse brains.

We found that ventral cortical regions L2/3 were more dense in left hemispheres, and several regions of the limbic system were both larger, and more cell dense, in males. In contrast, the prefrontal orbital cortex was more pronounced in females. Also, the outbred CD1 mouse strain sported larger cerebella, while inbred C57 mice had a particularly expansive olfactory system.

Variation across the population was considerable, though, and inter-individual variability was always greater than a single qualifier– even in these homogenous populations.

Out now in eLife: Elkind et al. 2023, “Sex, strain, and lateral differences in brain cytoarchitecture across a large mouse population”

And come explore the dataset!