Label-free, High-Resolution 3D Imaging and Machine Learning Analysis of Intestinal Organoids via Low-Coherence Holotomography

Accurate, label-free imaging of intestinal organoids is crucial for studying their morphology, growth dynamics, and responses to environmental stimuli. Holotomography (HT) provides high-resolution, three-dimensional (3D) visualization of live organoids without the need for fluorescent markers, thereby minimizing phototoxicity and preserving sample integrity. Real-time phase-based imaging allows continuous, label-free tracking of structural and functional changes. By using the refractive index as an intrinsic imaging contrast, this method enables quantification of biophysical properties such as volume, protein density, and protein content. The imaging data are further processed through machine learning-driven segmentation and feature extraction to support consistent, high-throughput analysis. This protocol details the complete experimental workflow for employing low-coherence HT in organoid research, covering organoid preparation, imaging acquisition, and machine learning-based data analysis. By integrating computational segmentation and quantitative assessments, this approach enables unbiased evaluation of key organoid properties, including viability, structural organization, and drug response. The ability to capture real-time morphological changes at subcellular resolution makes this protocol highly applicable to organoid-based studies in regenerative medicine, disease modeling, and pharmaceutical screening. The step-by-step methodology outlined here facilitates reproducibility and broad adaptation across different organoid systems.