Open AccessPosted Content
OMERO.mde in a use case for microscopy metadata harmonization: Facilitating FAIR principles in practical application with metadata annotation tools.
TLDR
MDEmic as discussed by the authors is a tool for editing metadata of microscopic imaging data in an easy and comfortable way that provides high flexibility in terms of adjustment of metadata sets, which is one of the major goals of FAIR principles.Abstract:
While the FAIR principles are well accepted in the scientific community, the implementation of appropriate metadata editing and transfer to ensure FAIR research data in practice is significantly lagging behind. On the one hand, it strongly depends on the availability of tools that efficiently support this step in research data management. On the other hand, it depends on the available standards regarding the interpretability of metadata. Here, we introduce a tool, MDEmic, for editing metadata of microscopic imaging data in an easy and comfortable way that provides high flexibility in terms of adjustment of metadata sets. This functionality was in great demand by many researchers applying microscopic techniques. MDEmic has already become a part of the standard installation package of the image database OMERO as OMERO.mde. This database helps to organize and visualize microscopic image data and keep track of their further processing and linkage to other data sets. For this reason, many imaging core facilities provide OMERO to their users. We present a use case scenario for the tailored application of OMERO.mde to imaging data of an institutional OMERO-based Membrane Dye Database, which requires specific experimental metadata. Similar to public image data repositories like the Image Data Resource, IDR, this database facilitates image data storage including rich metadata which enables data mining and re-use, one of the major goals of the FAIR principles.read more
Citations
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Journal ArticleDOI
Best practices and tools for reporting reproducible fluorescence microscopy methods.
Paula Montero Llopis,Rebecca A. Senft,Tim J. Ross-Elliott,Ryan Stephansky,Daniel P. Keeley,Preman Koshar,Guillermo Marqués,Ya-Sheng Gao,Benjamin R. Carlson,Thomas Pengo,Mark A. Sanders,Lisa A. Cameron,Michelle S. Itano +12 more
TL;DR: The authors provide guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities with the goal of improving microscopy reporting, rigor and reproducibility.
Journal ArticleDOI
QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
Glyn Nelson,Ulrike Boehm,Steve Bagley,Peter Bajcsy,Johanna Bischof,Claire M. Brown,Aurelien Dauphin,Ian M. Dobbie,John E Eriksson,Orestis Faklaris,Julia Fernandez-Rodriguez,Alexia Ferrand,Laurent Gelman,Ali Gheisari,Hella Hartmann,Christian Kukat,Alex Laude,Miso Mitkovski,Sebastian Munck,Alison J. North,Tobias M. Rasse,Ute Resch-Genger,Lucas C Schuetz,Arne Seitz,Caterina Strambio-De-Castillia,Jason R. Swedlow,Ioannis Alexopoulos,Karin Aumayr,Sergiy V. Avilov,Gert-Jan Bakker,Rodrigo R Bammann,Andrea Bassi,Hannes Beckert,Sebastian Beer,Yury Belyaev,Jakob Bierwagen,Konstantin A Birngruber,Manel Bosch,Juergen Breitlow,Lisa A. Cameron,Joe Chalfoun,James J. Chambers,Chieh-Li Chen,Eduardo Conde-Sousa,Alexander D. Corbett,Fabrice P. Cordelières,Elaine Del Nery,Ralf Dietzel,Frank Eismann,Elnaz Fazeli,Andreas Felscher,Hans-Ulrich Fried,Nathalie Gaudreault,Wah Ing Goh,Thomas Guilbert,Roland Hadleigh,Peter Hemmerich,Gerhard A Holst,Michelle S. Itano,Claudia B Jaffe,Helena Jambor,Stuart C Jarvis,Antje Keppler,David Kirchenbuechler,Marcel Kirchner,Norio Kobayashi,Gabriel Krens,Susanne Kunis,Judith Lacoste,Marco Marcello,Gabriel G. Martins,Daniel J Metcalf,Claire A. Mitchell,Joshua Moore,Tobias Mueller,Michael S. Nelson,Stephen Ogg,Shuichi Onami,Alexandra L Palmer,Perrine Paul-Gilloteaux,Jaime A. Pimentel,Laure Plantard,Santosh Podder,Elton Rexhepaj,Arnaud Royon,Markku Saari,Damien Schapman,Vincent Schoonderwoert,Britta Schroth-Diez,Stanley Schwartz,Michael Shaw,Martin Spitaler,Martin T Stoeckl,Damir Sudar,Jeremie Teillon,Stefan Terjung,Roland Thuenauer,Christian D Wilms,Graham D. Wright,Roland Nitschke +99 more
TL;DR: The QUAREP-LiMi initiative as mentioned in this paper aims to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
Posted ContentDOI
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model
Mathias Hammer,Maximiliaan Huisman,Alessandro Rigano,Ulrike Boehm,James J. Chambers,Nathalie Gaudreault,Alison J. North,Jaime A. Pimentel,Damir Sudar,Peter Bajcsy,Claire M. Brown,Alexander D. Corbett,Orestis Faklaris,Judith Lacoste,Alex Laude,Glyn Nelson,Roland Nitschke,Farzin Farzam,Carlas Smith,David Grunwald,Caterina Strambio-De-Castillia +20 more
TL;DR: The 4D Nucleome Initiative (4DN) and the BioImaging North America (BINA)-OME (NBO namespace) as mentioned in this paper have proposed a set of metadata specifications for light microscopy data that scale with experimental intent and with the complexity of the instrumentation and analytical requirements.
Journal ArticleDOI
MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text.
Posted ContentDOI
Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications [preprint]
Alex Rigano,Shannon Ehmsen,Serkan Utku Öztürk,Joel Ryan,Alexander Balashov,Mathias Hammer,Koray Kirli,Karl A. Bellvé,Ulrike Boehm,Claire M. Brown,James J. Chambers,Robert A. Coleman,Andrea Cosolo,Orestis Faklaris,Kevin E. Fogarty,Thomas Guilbert,Anna B Hamacher,Michelle S. Itano,Daniel P. Keeley,Kunis S,Judith Lacoste,Alex Laude,Willa Y. Ma,Marco Marcello,Paula Montero-Llopis,Glyn Nelson,Roland Nitschke,Jaime A. Pimentel,Stefanie Weidtkamp-Peters,Peter J. Park,Burak H. Alver,Grunwald D,Caterina Strambio-De-Castillia +32 more
TL;DR: Micro-Meta App as mentioned in this paper is an open-source software designed to facilitate the extraction and collection of relevant microscopy metadata, which can be used for documenting imaging experiments and shared with the community.
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Journal ArticleDOI
The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging
Ilya G. Goldberg,Chris Allan,Jean-Marie Burel,Doug Creager,Andrea Falconi,Harry Hochheiser,Josiah Johnston,Jeff Mellen,Peter K. Sorger,Jason R. Swedlow +9 more
TL;DR: The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.