Data underlying the PhD thesis: Shedding light on dynamic processes in the intestinal epithelium

This dataset contains data underlying the PhD dissertation of Willem Kasper Spoelstra, under supervision of (promotor) Prof. Dr. Ir. Sander J. Tans, Dr. Jeroen van Zon and (promotor) Prof. Dr. Pieter Rein ten Wolde. In this project, live-cell imaging and single-cell tracking was used to study several complex dynamic processes in intestinal organoids. These processes include cell extrusion (Chapter 2), onset of differentiation (Chapter 3), differentiation and function of rare human BEST4/CA7 cells (Chapter 4). Additionally, two additional chapters describe a new way to predict cell nuclei and membranes in organoids from brightfield images (Chapter 5), and protocols for doing long-term quantitative microscopy on intestinal organoids (Chapter 6). Tracking analyses were performed using a custom-built software (OrganoidTracker). This dataset contains .csv files necessary to replot the graphs in (co-)first author chapters (2, 4 and 6). Data for the other chapters (3 and 5) is available as per the data availability statement in the respective publications. The DOIs of these publications are included.