Hierarchical Bayesian modeling of multiregion 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 multiregion measurement, but because the imaging is done postmortem, 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 undersampled 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 multiregion 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 undersampled data.