Central nervous system atlas of larval zebrafish constructed using the morphology of single excitatory and inhibitory neurons
Comprehensive single-neuron mapping is essential for understanding the brain connectome. However, focusing only on mapping the projections of neurons from a single brain region gives limited insight into the global organizational principles of brain connectivity. Here, we present a whole body-wide Common Physical Space (CPSv1.0) for larval zebrafish, integrating neuroanatomical parcellations, cytoarchitecture atlases of excitatory (E) and inhibitory (I) neurons, and a dendrite-axon-annotated projectome comprising 12,219 E and 7,792 I neuronal morphologies (~25% of total E and I neurons). These neurons span all regions of the brain, spinal cord, and peripheral ganglia, forming 531 hierarchical morphotypes and generating weighted and directed inter-cell-type and inter-region connectomes. Projection and network analyses reveal structural divergence between E and I neurons, combinatory and modular projection rules, behavior-linked pathways, structured E and I connectivities, and multimodal sensorimotor hubs. Hosted on an open interactive platform, these digital atlases establish a scalable framework for multimodal neural data integration, offering insights into the global neural architecture across the whole central nervous system.