An atlas of functional ensembles in the zebrafish hindbrain links structural and molecular features to behavior

Abstract

The vertebrate hindbrain sustains functions essential for survival and behavioral control, yet how it operates as a whole remains poorly understood. Here we map its functional organization in larval zebrafish, whose transparency permits imaging of the entire hindbrain. We first curate established functional populations from the literature into an atlas annotated with putative mammalian counterparts. We then complement this library with ensembles of co-active neurons extracted without prior labels from whole-hindbrain light-field recordings in behaving larvae. We identify 70 ensembles that recur across individuals and recover most of them in independent light-sheet datasets. Ensembles also align with spatial gene-expression patterns and share their bilateral symmetry. Behavioral characterization identifies known eye- and tail-movement-related populations and reveals new associations with fin and mouth movements. Combining co-activity, molecular signatures, and neuronal projections suggests a candidate recurrent inter-regional circuit. Our atlas thus provides a common spatial reference for linking functional, molecular, and anatomical data to guide circuit discovery. HIGHLIGHTS hindbrain ensembles recur across fish, and most are robustly detected across methods ensembles match gene expression and share its bilateral symmetry track movement of multiple body parts around swimming onset maps link activity, molecular and projection data to guide circuit discovery