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MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text

dc.contributor.authorRyan, Joel
dc.contributor.authorPengo, Thomas
dc.contributor.authorRigano, Alex
dc.contributor.authorLlopis, Paula Montero
dc.contributor.authorItano, Michelle S.
dc.contributor.authorCameron, Lisa A.
dc.contributor.authorMarques, Guillermo
dc.contributor.authorStrambio-De-Castillia, Caterina
dc.contributor.authorSanders, Mark A.
dc.contributor.authorBrown, Claire M.
dc.date2022-08-11T08:10:18.000
dc.date.accessioned2022-08-23T17:03:24Z
dc.date.available2022-08-23T17:03:24Z
dc.date.issued2021-10-15
dc.date.submitted2021-11-01
dc.identifier.citation<p>Ryan J, Pengo T, Rigano A, Llopis PM, Itano MS, Cameron LA, Marqués G, Strambio-De-Castillia C, Sanders MA, Brown CM. MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text. Nat Methods. 2021 Oct 15. doi: 10.1038/s41592-021-01290-5. Epub ahead of print. PMID: 34654919. <a href="https://doi.org/10.1038/s41592-021-01290-5">Link to article on publisher's site</a></p>
dc.identifier.issn1548-7091 (Linking)
dc.identifier.doi10.1038/s41592-021-01290-5
dc.identifier.pmid34654919
dc.identifier.urihttp://hdl.handle.net/20.500.14038/44417
dc.description.abstractroper reporting of metadata is essential to reproduce microscopy experiments, interpret results and share images. The lack of methods reporting in microscopy is evident in that few research articles pass a test for the minimal information required to reproduce experiments (about 17% of 240 articles containing 1,500 figures with images). The problem is compounded by the number and variety of microscope modalities, options and associated components. Automation has distanced researchers from the technical parameters, so it can be difficult for them to know what information needs to be reported. MethodsJ2 is an ImageJ/Fiji-based software tool that aims to improve reproducibility in microscopy by capturing image metadata from multiple sources, consolidating it and automatically generating methods text for publication.
dc.language.isoen_US
dc.relation<p><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&list_uids=34654919&dopt=Abstract">Link to Article in PubMed</a></p>
dc.relation.urlhttps://doi.org/10.1038/s41592-021-01290-5
dc.subjectImaging
dc.subjectMicroscopy
dc.subjectResearch data
dc.subjectBiochemistry, Biophysics, and Structural Biology
dc.subjectBioimaging and Biomedical Optics
dc.subjectComputer Sciences
dc.subjectLaboratory and Basic Science Research
dc.subjectOptics
dc.titleMethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text
dc.typeJournal Article
dc.source.journaltitleNature methods
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/pmm_pp/150
dc.identifier.contextkey25697734
html.description.abstract<p>roper reporting of metadata is essential to reproduce microscopy experiments, interpret results and share images. The lack of methods reporting in microscopy is evident in that few research articles pass a test for the minimal information required to reproduce experiments (about 17% of 240 articles containing 1,500 figures with images). The problem is compounded by the number and variety of microscope modalities, options and associated components. Automation has distanced researchers from the technical parameters, so it can be difficult for them to know what information needs to be reported. MethodsJ2 is an ImageJ/Fiji-based software tool that aims to improve reproducibility in microscopy by capturing image metadata from multiple sources, consolidating it and automatically generating methods text for publication.</p>
dc.identifier.submissionpathpmm_pp/150
dc.contributor.departmentProgram in Molecular Medicine


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