The Twenty Questions of bioimage object analysis
The language used by microscopists who wish to find and measure objects in an image often differs in critical ways from that used by computer scientists who create tools to help them do this, making communication hard across disciplines. This work proposes a set of standardized questions that can gu...
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| Published in: | Nature methods Vol. 20; no. 7; pp. 976 - 978 |
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| Main Authors: | , |
| Format: | Journal Article |
| Language: | English |
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01.07.2023
Nature Publishing Group |
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| ISSN: | 1548-7091, 1548-7105, 1548-7105 |
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| Abstract | The language used by microscopists who wish to find and measure objects in an image often differs in critical ways from that used by computer scientists who create tools to help them do this, making communication hard across disciplines. This work proposes a set of standardized questions that can guide analyses and shows how it can improve the future of bioimage analysis as a whole by making image analysis workflows and tools more FAIR (findable, accessible, interoperable and reusable). |
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| AbstractList | The language used by microscopists who wish to find and measure objects in an image often differs in critical ways from that used by computer scientists who create tools to help them do this, making communication hard across disciplines. This work proposes a set of standardized questions that can guide analyses and shows how it can improve the future of bioimage analysis as a whole by making image analysis workflows and tools more FAIR (findable, accessible, interoperable and reusable). |
| Author | Cimini, Beth A. Eliceiri, Kevin W. |
| AuthorAffiliation | 1 Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA 2 Center for Quantitative Cell Imaging, University of Wisconsin–Madison and Morgridge Institute for Research, Madison, WI, USA |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37434006$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1038/sdata.2016.18 10.1038/nmeth.2019 10.1371/journal.pbio.3000340 10.1038/s41597-022-01710-x 10.1002/mrd.22489 10.1038/nmeth.4473 10.1186/s13326-016-0074-0 10.1002/1873-3468.14451 10.5281/zenodo.7654937 10.48550/arXiv.2302.07005 10.1038/s41592-021-01327-9 10.1186/s12859-021-04424-w 10.12688/f1000research.52569.1 10.7490/f1000research.1117826.1 10.1017/S2633903X21000039 10.1038/s41592-021-01166-8 |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 B.A.C. drafted the initial schema, coded the web tool and wrote the manuscript; K.W.E. revised the schema and the manuscript. Author contributions |
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| References | UlmanVNat. Methods201714114111521:CAS:528:DC%2BC2sXhslehtrbI10.1038/nmeth.4473290834035777536 SchindelinJNat. Methods201296766821:CAS:528:DC%2BC38XhtVKnurbJ10.1038/nmeth.201922743772 Biaflows. https://biaflows-sandbox.neubias.org/#/ (accessed 19 February 2023). Grand Challenge. https://grand-challenge.org/ (accessed 19 February 2023). Paul-GilloteauxPF1000 Res.20211032010.12688/f1000research.52569.1 JuppSJ. Biomed. Semantics201672810.1186/s13326-016-0074-0271951024870745 KalašMF1000 Res.202010.7490/f1000research.1117826.1 Jamali, N., Dobson, E. T. A., Eliceiri, K. W., Carpenter, A. E. & Cimini, B. A. Biol. Imaging1, e4 (2022). HammerMNat. Methods202118142714401:CAS:528:DC%2BB3MXis1OisrfM10.1038/s41592-021-01327-9348625019271325 WilkinsonMDSci. Data2016310.1038/sdata.2016.18269782444792175 BarkerMSci. Data2022910.1038/s41597-022-01710-x362417549562067 SchindelinJRuedenCTHinerMCEliceiriKWMol. Reprod. Dev.2015825185291:CAS:528:DC%2BC2MXhtFehtr%2FI10.1002/mrd.22489261533685428984 HaaseRFEBS Lett.2022596247224851:CAS:528:DC%2BB38XhvF2qsbbP10.1002/1873-3468.1445135833863 RuedenCTPLoS Biol.201917e300034010.1371/journal.pbio.3000340312162696602289 Cimini, B. Zenodohttps://doi.org/10.5281/zenodo.7654937 (2023). Stirling, D. R. et al. BMC Bioinformatics22, 433 (2021). Schmied, C. et al. Community-developed checklists for publishing images and image analysis. Preprint at https://doi.org/10.48550/arXiv.2302.07005 (2023). SarkansUNat. Methods202118141814221:CAS:528:DC%2BB3MXhtFCjur7M10.1038/s41592-021-01166-8340212808606015 J Schindelin (1919_CR12) 2015; 82 S Jupp (1919_CR6) 2016; 7 CT Rueden (1919_CR17) 2019; 17 M Hammer (1919_CR4) 2021; 18 1919_CR18 M Kalaš (1919_CR5) 2020 V Ulman (1919_CR14) 2017; 14 MD Wilkinson (1919_CR7) 2016; 3 R Haase (1919_CR11) 2022; 596 1919_CR15 J Schindelin (1919_CR13) 2012; 9 1919_CR16 P Paul-Gilloteaux (1919_CR2) 2021; 10 1919_CR10 M Barker (1919_CR8) 2022; 9 1919_CR9 1919_CR1 U Sarkans (1919_CR3) 2021; 18 |
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| Title | The Twenty Questions of bioimage object analysis |
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