Doghouse: a new assay to probe spatiotemporal dynamics of brain-wide activity

To analyze the data generated with whole-brain staining and imaging approaches, several assays have been proposed registering brain samples to atlases and detecting stained cells in individual brain regions. However, the algorithms for quantifying labeled cells in the brain and grounding these counts to the brain's functional anatomy are still in the early stages of development. To bridge this gap, we introduce DOGHOUSE, an end-to-end assay for probing spatiotemporal dynamics of brain-wide activity. The assay consists of two components. CORGI, a software package for registering whole- brain sample data in space and time, overcomes the differences between dissimilar perinatal brains. DALMATIAN, a software package for cell detection in whole-brain sample data, separates densely packed dividing cells. The staining protocol has been validated for the staining specificity whilst the software packages have shown competitive performance meeting or exceeding the state-of-the-art on diverse datasets. Our assay automates a variety of tasks including group comparison and monitoring brain development dynamics. All methods are available for download via open access.