Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

DC ElementWertSprache
dc.contributor.authorRigano, Alessandro
dc.contributor.authorEhmsen, Shannon
dc.contributor.authorOzturk, Serkan Utku
dc.contributor.authorRyan, Joel
dc.contributor.authorBalashov, Alexander
dc.contributor.authorHammer, Mathias
dc.contributor.authorKirli, Koray
dc.contributor.authorBoehm, Ulrike
dc.contributor.authorBrown, Claire M.
dc.contributor.authorBellve, Karl
dc.contributor.authorChambers, James J.
dc.contributor.authorCosolo, Andrea
dc.contributor.authorColeman, Robert A.
dc.contributor.authorFaklaris, Orestis
dc.contributor.authorFogarty, Kevin E.
dc.contributor.authorGuilbert, Thomas
dc.contributor.authorHamacher, Anna B.
dc.contributor.authorItano, Michelle S.
dc.contributor.authorKeeley, Daniel P.
dc.contributor.authorKunis, Susanne
dc.contributor.authorLacoste, Judith
dc.contributor.authorLaude, Alex
dc.contributor.authorMa, Willa Y.
dc.contributor.authorMarcello, Marco
dc.contributor.authorMontero-Llopis, Paula
dc.contributor.authorNelson, Glyn
dc.contributor.authorNitschke, Roland
dc.contributor.authorPimentel, Jaime A.
dc.contributor.authorWeidtkamp-Peters, Stefanie
dc.contributor.authorPark, Peter J.
dc.contributor.authorAlver, Burak H.
dc.contributor.authorGrunwald, David
dc.contributor.authorStrambio-De-Castillia, Caterina
dc.date.accessioned2021-12-23T16:24:12Z-
dc.date.available2021-12-23T16:24:12Z-
dc.identifier.issn15487091
dc.identifier.urihttps://osnascholar.ub.uni-osnabrueck.de/handle/unios/14810-
dc.description.abstractFor quality, interpretation, reproducibility and sharing value, microscopy images should be accompanied by detailed descriptions of the conditions that were used to produce them. Micro-Meta App is an intuitive, highly interoperable, open-source software tool that was developed in the context of the 4D Nucleome (4DN) consortium and is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes. Micro-Meta App is an intuitive, highly interoperable, open-source software tool designed to facilitate the extraction and collection of relevant microscopy metadata as specified by recent community guidelines.
dc.description.sponsorshipChan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation; NIHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [U01CA200059, 1U01EB021238, 8U01DA047733-05, 5R01GM126045-04]; NSFNational Science Foundation (NSF) [1917206]; Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation [2020-225398, 2019-198107]; National Infrastructure France BioImaging [ANR-10-INBS-04]; IBISA consortium; NIH-NINDS Neuroscience Center Support Grant [P30 NS045892, RRID:SCR_019060]; NIH-NICHD Intellectual and Developmental Disabilities Research Center Support Grant [P50 HD103573]; Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [180879236 INF, SFB 944]; Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)German Research Foundation (DFG) [Ni 451/9-1 MIAP-Freiburg, 267205415SFB 1208]; [2019-198155 (5022)]; We would like to thank L. Lifshitz at the Biomedical Imaging Group of the Program in Molecular Medicine at the University of Massachusetts Medical School for invaluable intellectual input and countless fruitful discussions and for his friendship, advice and steadfast support throughout the development of this project. We acknowledge M. Luban for critically reading and editing the manuscript. This project could never have been carried out without the leadership, insightful discussions, support and friendship of all OME consortium members, with particular reference to J. Swedlow, J. Moore, C. Allan, J.M. Burel and W. Moore. We are massively indebted to the RIKEN community for their fantastic work to bring open science into biology. We would like to particularly acknowledge N. Kobayashi and S. Onami for their friendship and support. We thank all members of Bioimaging North America, German Bioimaging, Euro-Bioimaging (in particular A. Keppler and F. Paina) and QUAREP-LiMi (in particular all members of the Working Group 7-Metadata; https://quarep.org/working-groups/wg-7-metadata/) for invaluable intellectual input, fruitful discussions and advice. We are also indebted to the following individuals for their continued and steadfast support: J. Luban, R. Davis and T. Pederson at the University of Massachusetts Medical School; J. Ritland, R. Singer and W. Zipfel of the 4D Nucleome Consortium; I. Fingerman, J. Satterlee, J. Mietz, R. Conroy and O. Blondel at the NIH. This work was supported by grant 2019-198155 (5022) awarded to C.S.-D.-C. by the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation, as part of their Imaging Scientist Program. Major funding also came from: (1) NIH grant U01CA200059 to P.J.P., C.S.-D.-C and D.G.; (2) NIH grants 1U01EB021238 and 8U01DA047733-05, and NSF grant 1917206 to D.G. C.M.B. was funded in part by grant 2020-225398 from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. R.A.C. was funded by NIH grant 5R01GM126045-04. T.G. and O.F. are members of the RTmfm network, and the MRI and IMAG'IC core facilities are supported by the National Infrastructure France BioImaging (grant ANR-10-INBS-04) and IBISA consortium. M.S.I. was supported by grant number 2019-198107, from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. The UNC Neuroscience Microscopy Core (RRID:SCR_019060) is supported, in part, by funding from the NIH-NINDS Neuroscience Center Support Grant P30 NS045892 and the NIH-NICHD Intellectual and Developmental Disabilities Research Center Support Grant P50 HD103573. SK was funded by the Deutsche Forschungsgemeinschaft: SFB 944 (Reference 180879236 INF). R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) grant Ni 451/9-1 MIAP-Freiburg. S.W.-P. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) project-ID 267205415SFB 1208, project INF.
dc.language.isoen
dc.publisherNATURE PORTFOLIO
dc.relation.ispartofNATURE METHODS
dc.subjectBiochemical Research Methods
dc.subjectBiochemistry & Molecular Biology
dc.subjectEXPERIMENT MIAME
dc.subjectHUMAN CELL ATLAS
dc.subjectIMAGE DATA
dc.subjectMINIMUM INFORMATION
dc.titleMicro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications
dc.typejournal article
dc.identifier.doi10.1038/s41592-021-01315-z
dc.identifier.isiISI:000725960800003
dc.contributor.orcid0000-0001-7471-2244
dc.contributor.orcid0000-0002-7295-815X
dc.contributor.orcid0000-0003-1622-663X
dc.contributor.orcid0000-0002-1069-1816
dc.contributor.orcid0000-0001-7734-3771
dc.contributor.orcid0000-0001-7374-8245
dc.contributor.researcheridB-1498-2008
dc.identifier.eissn15487105
dc.publisher.placeHEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY
dcterms.isPartOf.abbreviationNat. Methods
dcterms.oaStatushybrid
crisitem.author.deptCenter of Cellular Nanoanalytics Osnabrück-
crisitem.author.deptidresearchcenter3-
crisitem.author.orcid0000-0001-6523-7496-
crisitem.author.parentorgFB 05 - Biologie/Chemie-
crisitem.author.grandparentorgUniversität Osnabrück-
crisitem.author.netidKuSu652-
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