EpiTools, a napari Plugin for Quantifying Epithelial Dynamics

The plugin EpiTools (image processing toolkit for epithelia) was developed to address the challenges in analyzing dynamic microscopy images of epithelia, in which cells are tightly attached to each other and morphologically distinct from isolated cells. EpiTools is extremely useful for quantifying tissue dynamics, but it has become challenging to maintain due to its implementation in Matlab/Icy. There is also a lack of plugins on the napari hub that can target the analysis of epithelia.

This project seeks to port EpiTools into napari, so the image analysis community can segment, track, and quantitatively analyze dynamic cell shape and the packing of epithelial cells from 4D (3D + time) imaging data.