Hierarchical Bayesian modeling of multi-region brain cell count data

We can now collect cell-count data across whole animal brains quantifying recent neuronal activity, gene expression, or anatomical connectivity. This is a powerful approach since it is a multi-region measurement, but because the imaging is done post-mortem, each animal only provides one set of counts. Experiments are expensive and since cells are counted by imaging and aligning a large number of brain sections, they are time-intensive. The resulting datasets tend to be under-sampled with fewer animals than brain regions. As a consequence, these data are a challenge for traditional statistical approaches. We present a ‘standard’ partially-pooled Bayesian model for multi-region cell-count data and apply it to two example datasets. These examples demonstrate that hierarchical Bayesian methods are well suited to these data. In both cases the Bayesian model outperformed standard parallel t-tests. Overall, inference for cell-count data is substantially improved by the ability of the Bayesian approach to capture nested data and by its rigorous handling of uncertainty in under-sampled data.