{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Borten MA"],"funding":["NCI NIH HHS"],"pagination":["5319"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC5871765"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["8(1)"],"pubmed_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 m"],"journal":["Scientific reports"],"pubmed_title":["Automated brightfield morphometry of 3D organoid populations by OrganoSeg."],"pmcid":["PMC5871765"],"funding_grant_id":["R01 CA194470","U01 CA215794","P30 CA044579"],"pubmed_authors":["Clevers H","Bajikar SS","Sasaki N","Borten MA","Janes KA"],"additional_accession":[]},"is_claimable":false,"name":"Automated brightfield morphometry of 3D organoid populations by OrganoSeg.","description":"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 m","dates":{"release":"2018-01-01T00:00:00Z","publication":"2018 Mar","modification":"2026-05-04T02:41:27.248Z","creation":"2019-03-26T23:23:55Z"},"accession":"S-EPMC5871765","cross_references":{"pubmed":["29593296"],"doi":["10.1038/s41598-017-18815-8"]}}