Whole-brain co-mapping of neuronal activity and spatial transcriptomics at cellular resolution in behaving zebrafish reveals that molecular identity defined by gene co-expression organizes neurons into over 2,000 functional-genetic-anatomical subpopulations with specialized roles in sensory processing and motor control, and demonstrates that genetically-matched neurons exhibit enhanced activity correlations across the entire brain, establishing molecular identity as a fundamental organizing principle of brain-wide functional networks.

The brain’s capabilities rely on both the molecular properties of individual cells and their interactions across brain-wide networks. However, relating gene expression to activity in individual neurons across the entire brain remains elusive. Here we developed an experimental-computational platform, WARP, for whole-brain imaging of neuronal activity during behavior, expansion-assisted spatial transcriptomics, and cellular-level registration of these two modalities. Through joint analysis of whole-brain neuronal activity during multiple behaviors, cellular gene expression, and anatomy, we identified functions of molecularly defined populations—including luminance coding in a cckb-pou4f2 midbrain population and task-structured activity in pvalb7-eomesa hippocampal-like neurons—and defined over 2,000 other function-gene-anatomy subpopulations. Analysis of this unprecedented multimodal dataset also revealed that most gene-matched neurons showed stronger activity correlations, highlighting a brain-wide role for gene expression in functional organization. WARP establishes a foundational platform and open-access dataset for cross-experiment discovery, high-throughput function-to-gene mapping, unification of cell biology and systems neuroscience, and scalable circuit modeling at the whole-brain scale.