Multiplexed neuromodulatory-type-annotated whole-brain EM-reconstruction of larval zebrafish

Diverse neuromodulatory systems confer functional flexibility upon the hardwired sensorimotor pathways of the brain1-6. Among these, the evolutionarily conserved locus coeruleus (LC)-norepinephrinergic (NE) system integrates and broadcasts information globally7-9. While previous studies have primarily focused on its axonal outputs and effects on neural processing, the organizational logic of its synaptic inputs, enabling it to sense global brain states and in turn shape its activity dynamics for appropriate neuromodulation10,11, remains poorly explored. To address this, we mapped the synaptic input architecture of individual LC-NE neurons by establishing Fish-X, a whole-brain microscale reconstruction of larval zebrafish with neuron-type annotations. This dataset encompasses the retina, brain and anterior spinal cord, capturing >240,000 cells and >25 million synapses. Monoaminergic (including NE, dopaminergic, and serotonergic), hypocretinergic, and glycinergic neurons were resolved by multiplexed subcellular APEX2 labeling, while glutamatergic and GABAergic identities were inferred via morphology comparison with a zebrafish mesoscopic atlas12,13. Compared with other neuronal populations, LC-NE neurons display distinct perisomatic features and high dendritic indegrees. Reconstruction of near-complete dendritic inputs to individual LC-NE neurons reveals their broad yet sparse synaptic convergence across the brain. These synaptic inputs are not randomly distributed but instead organized according to sensory/motor modality, excitatory/inhibitory identity, and synaptic strength. Individual LC-NE neurons share common inputs, a feature conserved within and across monoaminergic systems, suggesting a co-innervation mechanism for coordinated neuromodulation. Thus, our study uncovers multi-level principles governing the spatial organization of LC-NE neurons broad-yet-sparse inputs and provides a pivotal resource for deciphering the microscale architecture of neuromodulatory systems.