We conducted a large-scale study of whole-brain morphometry, analyzing 3.7 peta-voxels of mouse brain images at the single-cell resolution, producing one of the largest multi-morphometry databases of mammalian brains to date. We spatially registered 204 mouse brains and associated data from six Brain Initiative Cell Census Network (BICCN) data sources covering three major imaging modalities from five collaborative projects to the Allen Common Coordinate Framework (CCF) atlas, annotated 3D locations of cell bodies of 182,497 neurons, modeled 15,441 dendritic microenvironments, characterized the full morphology of 1,876 neurons along with their axonal motifs, and detected 2.63 million axonal varicosities that indicate potential synaptic sites. Our analysis covers six levels of information related to neuronal populations, dendritic microenvironments, single-cell full morphology, sub-neuronal dendritic and axonal arborization, axonal varicosities , and sub-neuronal structural motifs, along with a quantification of the diversity and stereotypy of patterns at each level. We identified 15 modules consisting of intercorrelated brain regions selected from 314 anatomical areas in the CCF. Our analysis revealed the dendritic microenvironment as a powerful method for delineating region-specific cell types and potential subtypes. We also found that full neuronal morphologies can be categorized into four distinct classes based on spatially tuned morphological features, with substantial cross-areal diversity in dendritic arbors and axonal arbors, along with quantified stereotypy within cortical, thalamic, and striatal regions. We found the lamination of somas is more effective than the brain region of somas in differentiating neuron arbors within the cortex. Further analysis of diverging and converging projections of individual neurons in 25 brain regions throughout the brain reveals branching preferences in the brain-wide and local distributions of axonal varicosities . Overall, our study provides a comprehensive description of key anatomical structures of neurons and their types, covering a wide range of scales and features, and contributes an extensive resource to understanding neuronal diversity in the mammalian brain.
