Organoid Morphology Analysis

Organoid morphology analysis is the systematic evaluation of three-dimensional, stem cell-derived tissue models by examining their structure, organization, and visual features. Using microscopy and image analysis, researchers quantify characteristics such as size, shape, circularity, branching, lumen formation, and cellular architecture, often comparing changes across culture conditions or treatments. In cancer research, these measurements help characterize patient-derived organoids, assess tumor heterogeneity, and track responses to drugs or genetic perturbations. Morphological profiles provide reproducible phenotypic readouts that complement molecular assays, supporting disease modeling, treatment evaluation, and the development of more predictive preclinical research systems.

Organoid Morphology Analysis - Related Videos

Research

JoVE EoE - Viral Growth and Techniques

Processing of Lentivirus-Transduced Mouse Intestinal Organoids for Immunohistochemical Analysis

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2026

Source: Van Lidth de Jeude, J. F., et al. A Protocol for Lentiviral Transduction and Downstream Analysis of Intestinal Organoids. J. Vis. Exp. (2015).This video demonstrates the processing of lentivirus-transduced mouse intestinal organoids for paraffin embedding, to enable their downstream analysis for assessing gene expression.

Generation and Single-Cell Transcriptomic Analysis of Hepatocellular Carcinoma Organoids following Drug Treatment

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2026

This protocol outlines a streamlined method for generating hepatocellular carcinoma organoids, applying drug treatment, and performing single-cell RNA sequencing before and after treatment to characterize treatment-associated transcriptional changes.

Rectal Organoid Morphology Analysis (ROMA): A Diagnostic Assay in Cystic Fibrosis

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2022

This protocol describes rectal organoid morphology analysis (ROMA), a novel diagnostic assay for cystic fibrosis (CF). Morphological characteristics, namely the roundness (circularity index, CI) and the presence of a lumen (intensity ratio, IR), are a measure of CFTR function. Analysis of 189 subjects showed perfect discrimination between CF and non-CF.

A Protocol for Lentiviral Transduction and Downstream Analysis of Intestinal Organoids

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Cited by 81 •

2015

In this video protocol we give a step by step explanation of lentiviral transduction in organoids of primary intestinal epithelium and of processing and downstream analysis of these cultures by quantitative RT-PCR, RNA-microarray and immunohistochemistry.

Research

JoVE Journal - Cancer Research
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Multiparametric Tumor Organoid Drug Screening Using Widefield Live-Cell Imaging for Bulk and Single-Organoid Analysis

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Cited by 14 •

2022

This protocol describes a semi-automated method for medium- to high-throughput organoid drug screenings and microscope-agnostic, automated image analysis software to quantify and visualize multiparametric, single-organoid drug responses to capture intratumor heterogeneity.

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