Automated brightfield morphometry of 3D organoid populations by OrganoSeg.
Publication/Presentation Date
3-28-2018
Abstract
Spheroid and organoid cultures are powerful in vitro models for biology, but size and shape diversity within the culture is largely ignored. To streamline morphometric profiling, we developed OrganoSeg, an open-source software that integrates segmentation, filtering, and analysis for archived brightfield images of 3D culture. OrganoSeg is more accurate and flexible than existing platforms, and we illustrate its potential by stratifying 5167 breast-cancer spheroid and 5743 colon and colorectal-cancer organoid morphologies. Organoid transcripts grouped by morphometric signature heterogeneity were enriched for biological processes not prominent in the original RNA sequencing data. OrganoSeg enables complete, objective quantification of brightfield phenotypes, which may give insight into the molecular and multicellular mechanisms of organoid regulation.
Volume
8
Issue
1
First Page
5319
Last Page
5319
ISSN
2045-2322
Published In/Presented At
Borten, M. A., Bajikar, S. S., Sasaki, N., Clevers, H., & Janes, K. A. (2018). Automated brightfield morphometry of 3D organoid populations by OrganoSeg. Scientific reports, 8(1), 5319. https://doi.org/10.1038/s41598-017-18815-8
Disciplines
Medicine and Health Sciences
PubMedID
29593296
Department(s)
Department of Medicine, Department of Medicine Fellows and Residents, Fellows and Residents
Document Type
Article