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. |
| References: | Curr Opin Syst Biol. 2018 Aug;10:43-52. (PMID: 30159406) Nat Rev Drug Discov. 2022 Dec;21(12):899-914. (PMID: 35637317) Trends Cell Biol. 2023 Jul;33(7):538-554. (PMID: 36623998) Curr Opin Biotechnol. 2016 Jun;39:134-142. (PMID: 27089218) Nat Methods. 2017 Aug 31;14(9):849-863. (PMID: 28858338) SLAS Discov. 2023 Oct;28(7):292-305. (PMID: 37666456) Nat Commun. 2023 Mar 13;14(1):1364. (PMID: 36914634) Cell Death Discov. 2023 Jul 31;9(1):277. (PMID: 37524741) Nat Methods. 2012 Jun 28;9(7):676-82. (PMID: 22743772) Cell Syst. 2022 Nov 16;13(11):911-923.e9. (PMID: 36395727) BMC Bioinformatics. 2021 Sep 10;22(1):433. (PMID: 34507520) |
| 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: 20240718 |
| رمز التحديث: | 20240718 |
| مُعرف محوري في PubMed: | PMC10690292 |
| PMID: | 38045474 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2331-8422 |
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