Automated 3D Morphometric Analysis Reveals Nuclear Hypertrophy and Reduced Cell Density in cdh2-Deficient Zebrafish Embryos

The mechanical regulation of nuclear volume is a fundamental yet under-explored aspect of embryogenesis. We developed an automated computational framework in Python to quantify 3D nuclear morphometry in zebrafish (Danio rerio) embryos. Applying this pipeline to cdh2-CRISPR mutant image stacks from the BioImage Archive (Accession: S-BIAD1405), we observed pronounced nuclear hypertrophy associated with reduced cadherin-mediated adhesion. Using voxel scaling factors verified in ImageJ (pixel width/height = 0.991492 µm; z spacing = 1.0 µm; consistent across WT and mutant stacks), we observed a ≈12.0% increase in median nuclear volume (1,606 vs. 1,434 voxels; Mann–Whitney U, p = 0.0407), while nearest-neighbor distances remained broadly similar, suggesting that local packing is comparatively preserved. These results support a model in which cadherin-dependent mechanical coupling contributes to nuclear size homeostasis. We provide biological insight into the mechanobiological role of cdh2 and an open-source workflow for reproducible volumetric analysis in complex 3D biological systems.