Journal
SCIENTIFIC REPORTS
Volume 8, Issue -, Pages -Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41598-017-18815-8
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Funding
- N.I.H. [U01-CA215794, R01-CA194470]
- UVA Cancer Center
- Ivy Foundation
- David and Lucile Packard Foundation [2009-34710]
- AMED-CREST
- JSPS KAKENHI [17844632]
- American Association for Cancer Research [SU2C-AACR-DT1213]
- Dutch Cancer Society [HUBR KWF 2014-6917]
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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.
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