DeProj

DeProj is a MATLAB toolbox for quantitative morphometric analysis of epithelial tissues imaged in 3D. It addresses a common workflow in developmental and cell biology where a 3D volume is first projected onto a 2D plane to simplify cell segmentation, but where the projection can (i) reduce object visibility due to surrounding out-of-plane signal and (ii) introduce substantial geometric distortions that bias morphology measurements.

DeProj operates downstream of a surface-projection step by combining two inputs: (1) a height map describing the epithelial surface in the original 3D stack (e.g., produced by tools such as LocalZProjector), and (2) a cell segmentation performed on the corresponding 2D projection. Using the height map as a spatial correspondence between 2D projection coordinates and the 3D tissue surface, DeProj reconstructs the segmented cell contours on the curved surface, effectively lifting (“deprojecting”) the 2D segmentation back into 3D. It then computes morphology descriptors corrected for projection distortion, yielding more accurate measurements of cell shape and tissue geometry, including in highly curved specimens. The toolbox is designed to be broadly applicable across epithelial imaging datasets and to improve measurement fidelity relative to analyses performed directly on distorted 2D projections.