VoxHunt

The software tool 'VoxHunt' addresses the complexity of self-organizing brain tissues cultivated from human stem cells, commonly known as brain organoids or spheroids. These in vitro models provide insights into brain development, diseases, and evolution. However, the cellular diversity within and across individual organoids presents a challenge. 'VoxHunt' introduces a computational approach that utilizes three-dimensional in situ hybridization data from the Allen Brain Atlas for systematic comparisons. This tool enables the assessment of brain organoid patterning, developmental stages, and cellular composition. By comparing cellular transcriptomes and chromatin landscapes to spatial transcript patterns in the developing mammalian brain, 'VoxHunt' characterizes and visualizes the compositions of organoid cells. The tool is valuable for evaluating novel organoid engineering techniques and annotating emerging cell fates resulting from genetic and environmental perturbations within organoids.