Methods for Processing Stem Cell-Derived Organoids for Histological and Immunofluorescence Staining

Intestinal stem cell (ISC)-derived organoids provide a physiologically relevant 3D culture system to model intestinal biology, regeneration, and disease mechanisms. Their complex architecture, recapitulating crypt structures, poses challenges for downstream histological and immunohistochemical analyses, necessitating optimized processing, and staining protocols. Here, we describe robust workflows for the fixation, embedding, sectioning, and staining of ISC-derived organoids. Each method is detailed stepwise, with emphasis on preserving morphology and antigenicity. We discuss reagent choices, critical technical considerations, and troubleshooting tips to maximize data reproducibility and quality. We have integrated recent advances and best practices, serving as a comprehensive guide for researchers working with intestinal organoids.