Signatures of brain-wide functional maturation in larval zebrafish

Abstract

Brain development involves the coordinated organization of cellular activity into distributed functional networks, yet how this organization emerges across an entire vertebrate brain remains poorly understood. Here, we combined brain-wide structural and functional imaging to characterize brain maturation in larval zebrafish from 4 to 8 days post-fertilization. Brain growth was regionally heterogeneous and accompanied by progressive remodeling of mesoscale functional networks, with functional connectivity strengthening or weakening within distinct subnetworks. Spontaneous activity became more correlated in regions exhibiting pronounced neurogenesis, as revealed by HaloTag-based neuronal birthdating. Functional interactions became progressively less constrained by physical distance, while network organization became more modular, suggesting that long-range functional integration develops alongside increasing segregation of large-scale brain systems. At the cellular level, neuronal activity consolidated into larger, more modular functional ensembles whose combinations increasingly differentiated mesoscale modules. Visually responsive neurons redistributed along visual processing pathways, becoming more prevalent in regions further removed from retinal input, while motor-related activity declined broadly across the brain. The forebrain emerged as a major locus of maturation, exhibiting substantial anatomical expansion and a growing population of neurons displaying intrinsic activity fluctuations distinct from sensory and motor processes. Together, these findings reveal coordinated anatomical, cellular, and network-level signatures of early vertebrate brain maturation.