Tissue clearing methods allow every cell in the mouse brain to be imaged without physical sectioning. However, the computational tools currently available for cell quantification in cleared tissue images have been limited to counting sparse cell populations in stereotypical mice. Here we introduce NuMorph, a group of image analysis tools to quantify all nuclei and nuclear markers within the mouse cortex after tissue clearing and imaging by a conventional light-sheet microscope. We applied NuMorph to investigate a Topoisomerase 1 ( Top1 ) conditional knockout mouse model with severe brain structure deficits and identified differential effects of Top1 deletion on cortical cell-types and structures that were associated with spatial patterns of long gene expression. These tools are applicable for the study of 3D cellular level structural deficits in brains from other animal models of neuropsychiatric disorders. ### Competing Interest Statement The authors have declared no competing interest.

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