Quantitative imaging of dynamic processes in intestinal organoids

Organoids are powerful models for studying tissue dynamics across multiple cellular generations and offer key insights into organ homeostasis, cellular differentiation and disease. Live imaging of organoids is an essential tool for understanding dynamic processes on the cell level, while still in the tissue context. It allows for simultaneous quantification of gene expression and reconstruction of lineage trees, while tracking cells over space and time. Here, we present protocols for long-term imaging and quantitative analysis of intestinal organoids. Our workflow consists of sample preparation, experimental manipulations (such as drug treatments, laser ablations and fluorescence recovery after photobleaching), long-term live imaging (120 h), in situ fixation and permeabilization, multiplexed antibody staining and single-cell tracking with lineage reconstruction. The workflow is broadly applicable to studying dynamic cellular processes in both 2D and 3D organoids, at timescales from minutes to days. We outline strategies for optimizing organoid health, imaging conditions and experimental interventions to ensure efficient downstream analysis. In addition, we describe how this workflow enables real-time quantification of gene expression using fluorescent reporters and inferring cell type changes by combining multiplexed antibody staining with cell-tracking data. The skills required for following these protocols are organoid culturing and standard live-cell confocal microscopy, and the full experimental protocol takes ~2 weeks. Together, these protocols provide a comprehensive approach for studying cellular behavior, lineage trees, expression dynamics and cell–cell interactions in organoids.