Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications
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dc.contributor.author | Rigano, Alessandro | |
dc.contributor.author | Ehmsen, Shannon | |
dc.contributor.author | Ozturk, Serkan Utku | |
dc.contributor.author | Ryan, Joel | |
dc.contributor.author | Balashov, Alexander | |
dc.contributor.author | Hammer, Mathias | |
dc.contributor.author | Kirli, Koray | |
dc.contributor.author | Boehm, Ulrike | |
dc.contributor.author | Brown, Claire M. | |
dc.contributor.author | Bellve, Karl | |
dc.contributor.author | Chambers, James J. | |
dc.contributor.author | Cosolo, Andrea | |
dc.contributor.author | Coleman, Robert A. | |
dc.contributor.author | Faklaris, Orestis | |
dc.contributor.author | Fogarty, Kevin E. | |
dc.contributor.author | Guilbert, Thomas | |
dc.contributor.author | Hamacher, Anna B. | |
dc.contributor.author | Itano, Michelle S. | |
dc.contributor.author | Keeley, Daniel P. | |
dc.contributor.author | Kunis, Susanne | |
dc.contributor.author | Lacoste, Judith | |
dc.contributor.author | Laude, Alex | |
dc.contributor.author | Ma, Willa Y. | |
dc.contributor.author | Marcello, Marco | |
dc.contributor.author | Montero-Llopis, Paula | |
dc.contributor.author | Nelson, Glyn | |
dc.contributor.author | Nitschke, Roland | |
dc.contributor.author | Pimentel, Jaime A. | |
dc.contributor.author | Weidtkamp-Peters, Stefanie | |
dc.contributor.author | Park, Peter J. | |
dc.contributor.author | Alver, Burak H. | |
dc.contributor.author | Grunwald, David | |
dc.contributor.author | Strambio-De-Castillia, Caterina | |
dc.date.accessioned | 2021-12-23T16:24:12Z | - |
dc.date.available | 2021-12-23T16:24:12Z | - |
dc.identifier.issn | 15487091 | |
dc.identifier.uri | https://osnascholar.ub.uni-osnabrueck.de/handle/unios/14810 | - |
dc.description.abstract | For 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.sponsorship | Chan 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.iso | en | |
dc.publisher | NATURE PORTFOLIO | |
dc.relation.ispartof | NATURE METHODS | |
dc.subject | Biochemical Research Methods | |
dc.subject | Biochemistry & Molecular Biology | |
dc.subject | EXPERIMENT MIAME | |
dc.subject | HUMAN CELL ATLAS | |
dc.subject | IMAGE DATA | |
dc.subject | MINIMUM INFORMATION | |
dc.title | Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications | |
dc.type | journal article | |
dc.identifier.doi | 10.1038/s41592-021-01315-z | |
dc.identifier.isi | ISI:000725960800003 | |
dc.contributor.orcid | 0000-0001-7471-2244 | |
dc.contributor.orcid | 0000-0002-7295-815X | |
dc.contributor.orcid | 0000-0003-1622-663X | |
dc.contributor.orcid | 0000-0002-1069-1816 | |
dc.contributor.orcid | 0000-0001-7734-3771 | |
dc.contributor.orcid | 0000-0001-7374-8245 | |
dc.contributor.researcherid | B-1498-2008 | |
dc.identifier.eissn | 15487105 | |
dc.publisher.place | HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY | |
dcterms.isPartOf.abbreviation | Nat. Methods | |
dcterms.oaStatus | hybrid | |
crisitem.author.dept | Center of Cellular Nanoanalytics Osnabrück | - |
crisitem.author.deptid | researchcenter3 | - |
crisitem.author.orcid | 0000-0001-6523-7496 | - |
crisitem.author.parentorg | FB 05 - Biologie/Chemie | - |
crisitem.author.grandparentorg | Universität Osnabrück | - |
crisitem.author.netid | KuSu652 | - |
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geprüft am 06.06.2024