دورية أكاديمية
Reproducible image-based profiling with Pycytominer.
العنوان: | Reproducible image-based profiling with Pycytominer. |
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المؤلفون: | Serrano E; Department of Biomedical Informatics, University of Colorado School of Medicine., Chandrasekaran SN; Imaging Platform, Broad Institute of MIT and Harvard., Bunten D; Department of Biomedical Informatics, University of Colorado School of Medicine., Brewer KI; Independent Researcher., Tomkinson J; Department of Biomedical Informatics, University of Colorado School of Medicine., Kern R; Department of Biomedical Informatics, University of Colorado School of Medicine.; Case Western Reserve University., Bornholdt M; Imaging Platform, Broad Institute of MIT and Harvard., Fleming S; Data Sciences Platform, Broad Institute of MIT and Harvard., Pei R; Imaging Platform, Broad Institute of MIT and Harvard., Arevalo J; Imaging Platform, Broad Institute of MIT and Harvard., Tsang H; Imaging Platform, Broad Institute of MIT and Harvard., Rubinetti V; Department of Biomedical Informatics, University of Colorado School of Medicine., Tromans-Coia C; Imaging Platform, Broad Institute of MIT and Harvard., Becker T; Imaging Platform, Broad Institute of MIT and Harvard., Weisbart E; Imaging Platform, Broad Institute of MIT and Harvard., Bunne C; Imaging Platform, Broad Institute of MIT and Harvard., Kalinin AA; Imaging Platform, Broad Institute of MIT and Harvard., Senft R; Imaging Platform, Broad Institute of MIT and Harvard., Taylor SJ; Department of Biomedical Informatics, University of Colorado School of Medicine., Jamali N; Imaging Platform, Broad Institute of MIT and Harvard., Adeboye A; Imaging Platform, Broad Institute of MIT and Harvard., Abbasi HS; Imaging Platform, Broad Institute of MIT and Harvard., Goodman A; Imaging Platform, Broad Institute of MIT and Harvard.; Genentech gRED., Caicedo JC; Imaging Platform, Broad Institute of MIT and Harvard.; Morgridge Institute for Research, University of Wisconsin-Madison., Carpenter AE; Imaging Platform, Broad Institute of MIT and Harvard., Cimini BA; Imaging Platform, Broad Institute of MIT and Harvard., Singh S; Imaging Platform, Broad Institute of MIT and Harvard., Way GP; Department of Biomedical Informatics, University of Colorado School of Medicine. |
المصدر: | ArXiv [ArXiv] 2024 Jul 02. Date of Electronic Publication: 2024 Jul 02. |
نوع المنشور: | Journal Article; Preprint |
اللغة: | English |
بيانات الدورية: | Country of Publication: United States NLM ID: 101759493 Publication Model: Electronic Cited Medium: Internet ISSN: 2331-8422 (Electronic) Linking ISSN: 23318422 NLM ISO Abbreviation: ArXiv Subsets: PubMed not MEDLINE |
مستخلص: | Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To process these single-cells for downstream applications, we present Pycytominer, a user-friendly, open-source python package that implements the bioinformatics steps, known as "image-based profiling". We demonstrate Pycytominer's usefulness in a machine learning project to predict nuisance compounds that cause undesirable cell injuries. Competing Interests: Disclosure of competing interests The authors declare they have no competing interests relevant to this work. |
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معلومات مُعتمدة: | R35 GM122547 United States GM NIGMS NIH HHS; T15 LM009451 United States LM NLM NIH HHS |
تواريخ الأحداث: | Date Created: 20231204 Latest Revision: 20240904 |
رمز التحديث: | 20240904 |
مُعرف محوري في PubMed: | PMC10690292 |
PMID: | 38045474 |
قاعدة البيانات: | MEDLINE |
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