Automated Segmentation of Intestinal Organoid Cells and Nuclei

Summary

In a pilot study, the lab of Dr. Prisca Liberali, at Friedrich Miescher Institute, Switzerland, acquired a complete serial block-face electron microscopy stack of an intestinal organoid.

We developed a deep-learning pipeline for the automated segmentation of all organoid cells and their nuclei. The accurate segmentation of the thin filopodia of these cells was particularly challenging. (Sample preparation and data acquisition: Dr. Christel Genoud)