Cell-type-specific computational neuroanatomy, simulations from the sagittal and coronal Allen Brain Atlas

The Allen Atlas of the adult mouse brain is a brain-wide, genome-wide data set that has been made available online, triggering a renaissance in neuroanatomy. In particular, it has been used to define brain regions in a computational, data-driven way, and to estimate the region-specificity of cell types characterized independently by their transcriptional activity. However, these results were based on one series of co-registered (coronal) ISH image series per gene, whereas the online ABA contains several image series per genes, including sagittal ones. Since the sagittal series cover mostly the left hemisphere, we can simulate the variability of results by repeatedly drawing a random image series for each gene and restricting the computation to the left hemisphere. This gives rise to an estimate of error bars on the results of computational neuroanatomy. This manuscript is a complement to the paper Computational neuroanatomy: mapping cell-type densities in the mouse brain, simulations from the Allen Brain Atlas prepared for the International Conference on Mathematical Modeling in Physical Sciences June 5-8, 2015, Mykonos Island, Greece. 1 ar X iv :1 50 5. 06 43 4v 1 [ qbi o. N C ] 2 4 M ay 2 01 5 Acronyms. ABA: Allen Brain Atlas; ARA: Allen Reference Atlas; ISH: in situ hybridization.