@article{c7c12f7332174932aa7134de26c751fc,
title = "Automated brightfield morphometry of 3D organoid populations by OrganoSeg",
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.",
author = "Borten, {Michael A.} and Bajikar, {Sameer S.} and Nobuo Sasaki and Hans Clevers and Janes, {Kevin A.}",
note = "Funding Information: We thank A. Ewald, S. Muthuswamy, A. Bouton, and M. Karthikeyan for providing images, A. Koeppel and S. Turner from the UVA Bioinformatics Core (#P30-CA044579) for assistance with RNA sequencing alignments, and G. Rohde and J. Saucerman for comments on the manuscript. This work was supported by N.I.H. #U01-CA215794 and #R01-CA194470 (K.A.J.), a Women{\textquoteright}s 4-miler Breast Cancer Research Award from the UVA Cancer Center (K.A.J.), a Biomedical Innovation Grant from the Ivy Foundation (K.A.J.), the David and Lucile Packard Foundation #2009-34710 (K.A.J.), AMED-CREST (N.S.), JSPS KAKENHI #17844632 (N.S.), a Lotte Shigemitsu prize (N.S.), the American Association for Cancer Research #SU2C-AACR-DT1213 (H.C.), and the Dutch Cancer Society #HUBR KWF 2014-6917 (H.C.). Publisher Copyright: {\textcopyright} 2018 The Author(s).",
year = "2018",
month = dec,
day = "1",
doi = "10.1038/s41598-017-18815-8",
language = "English",
volume = "8",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",
}