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OrgLine: A versatile pipeline for organoid morphometry using detector-guided prompts.

Xun Deng¹, Xinyu Hao², Thomas Herget³

¹The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China; University of Chinese Academy of Sciences, Beijing, China.

Cell Reports Methods

|June 8, 2026

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This summary is machine-generated.

OrgLine is a new quantitative analysis pipeline for patient-derived organoids. This tool automates the analysis of organoid morphology from bright-field images, improving disease modeling and drug development.

Area of Science:

Biotechnology
Bioinformatics
Cell Biology

Background:

Patient-derived organoids are vital tools in disease modeling, drug development, and precision medicine.
Manual analysis of organoids in 3D culture is challenging and prone to artifacts in bright-field images.
Quantitative assessment of organoid morphology is crucial but complicated by imaging limitations.

Purpose of the Study:

To develop an automated quantitative analysis pipeline for patient-derived organoids.
To address the limitations of manual workflows and image artifacts in organoid analysis.
To enable accurate morphological characterization and segmentation of organoids.

Main Methods:

Development of OrgLine, a quantitative analysis pipeline for organoids.

Keywords:

CP: imaging CP: stem cell automation bright-field images cultivation organoids pipeline pre-trained quantitative segmentation stem cell

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Utilizing a large, curated dataset of bright-field organoid images.

Implementation of a detector coupled with a prompt-guided segmentation module.

Main Results:

OrgLine accurately recognizes organoids in bright-field images.
The pipeline enables quantitative characterization of morphological phenotypes across developmental stages.
Accurate instance segmentation for downstream morphometric assessment is achieved.

Conclusions:

OrgLine facilitates more automated and quantitative organoid cultivation workflows.
The pipeline enhances the utility of patient-derived organoids in research and clinical applications.
OrgLine improves the reliability and efficiency of organoid analysis.