CartoCell, a high-content pipeline for accurate 3D image analysis, unveils cell morphology patterns in epithelial cysts.

CartoCell is a deep learning-based image processing pipeline for the high-content segmentation of whole epithelial cysts acquired at low resolution with minimal human intervention. This pipeline enables high-precision cell segmentation that allows a single cell cartography study of major interest for the search of cellular patterns.

All the pipeline code, feature extraction, and the various single-cell cartography analysis tools are linked below.

The image dataset used can be found in this repository.

All directories mentioned in "steps to reproduce" refer to the release from ComplexOrganizationOfLivingMatter repository named:
Andrés San-Román et al. NaturalVariation-CartoCell_SingleCellCartographyTools_1.0.0CartoCell
https://github.com/ComplexOrganizationOfLivingMatter/NaturalVariation/releases/tag/CartoCell_SingleCellCartographyTools_1.0.0