Metadata (14)#
EDAM-bioimaging: The ontology of bioimage informatics operations, topics, data, and formats (update 2020)#
Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A Kirschmann, Anatole Chessel, Leandro Scholz, Fabianne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux
Licensed CC-BY-4.0
Tags: Metadata
Content type: Publication, Poster
FAIR High Content Screening in Bioimaging#
Rohola Hosseini, Matthijs Vlasveld, Joost Willemse, Bob van de Water, Sylvia E. Le Dévédec, Katherine J. Wolstencroft
Published 2023-07-17
Licensed CC-BY-4.0
The authors show the utility of Minimum Information for High Content Screening Microscopy Experiments (MIHCSME) for High Content Screening (HCS) data using multiple examples from the Leiden FAIR Cell Observatory, a Euro-Bioimaging flagship node for high content screening and the pilot node for implementing FAIR bioimaging data throughout the Netherlands Bioimaging network.
Tags: FAIR-Principles, Metadata, Research Data Management, Image Data Management, Bioimage Data
Content type: Publication
I3D bio – Information Infrastructure for BioImage Data - Bioimage Metadata#
Christian Schmidt
Licensed UNKNOWN
A Microscopy Research Data Management Resource.
Tags: Metadata, I3Dbio, Research Data Management, Bioimage Data
Content type: Collection
https://gerbi-gmb.de/i3dbio/i3dbio-rdm/i3dbio-bioimage-metadata/
MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community#
Susanne Kunis, Sebastian Hänsch, Christian Schmidt, Frances Wong, Caterina Strambio-De-Castillia, Stefanie Weidtkamp-Peters
Licensed ALL RIGHTS RESERVED
Tags: Research Data Management, Metadata
Content type: Publication
Metadata matters: access to image data in the real world#
Melissa Linkert, et al.
Published 2010
Tags: Metadata
Content type: Publication
https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real
MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text#
Joel Ryan, Thomas Pengo, Alex Rigano, Paula Montero Llopis, Michelle S. Itano, Lisa A. Cameron, Guillermo Marqués, Caterina Strambio-De-Castillia, Mark A. Sanders, Claire M. Brown
Tags: Metadata
Content type: Publication
Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications#
Alessandro Rigano, et al.
Tags: Metadata
Content type: Publication
Modeling community standards for metadata as templates makes data FAIR#
Mark A Musen, Martin J O’Connor, Erik Schultes, Marcos Martínez-Romero, Josef Hardi, John Graybeal
Published 2022-11-12
Licensed CC-BY-4.0
The authors have developed a model for scientific metadata, and they have made that model usable by both CEDAR and FAIRware. The approach shows that a formal metadata model can standardize reporting guidelines and that it can enable separate software systems to assist (1) in the authoring of standards-adherent metadata and (2) in the evaluation of existing metadata.
Tags: Data Stewardship, FAIR-Principles, Metadata
Content type: Publication
REMBI - Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology#
Ugis Sarkans, Wah Chiu, Lucy Collinson, Michele C. Darrow, Jan Ellenberg, David Grunwald, et al.
Published 2021-05-21
Licensed UNKNOWN
Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. The authors propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy.
Tags: Metadata, Bioimage Data, Image Data Management, Research Data Management
Content type: Publication
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015/
REMBI Overview#
Licensed CC0-1.0
Recommended Metadata for Biological Images (REMBI) provides guidelines for metadata for biological images to enable the FAIR sharing of scientific data.
Tags: FAIR-Principles, Metadata, Image Data Management, Research Data Management, Bioimage Data
Content type: Collection
Reporting and reproducibility in microscopy#
Published 2021-12-03
Licensed UNKNOWN
This Focus issue features a series of papers offering guidelines and tools for improving the tracking and reporting of microscopy metadata with an emphasis on reproducibility and data re-use.
Tags: Reproducibility, Metadata, Bioimage Data
Content type: Collection
Ten simple rules for making training materials FAIR#
Leyla Garcia, Bérénice Batut, Melissa L. Burke, Mateusz Kuzak, Fotis Psomopoulos, et al.
Published 2020-05-21
Licensed CC-BY-4.0
The authors offer trainers some simple rules, to help make their training materials FAIR, enabling others to find, (re)use, and adapt them.
Tags: Metadata, Bioinformatics, FAIR-Principles, Training
Content type: Publication
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854
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, et al.
Published 2022-07-10
Licensed UNKNOWN
Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose light Microscopy Metadata specifications that extend the OME data model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments.
Tags: Reproducibility, Microscopy Image Analysis, Metadata, Image Data Management, Bioimage Data
Content type: Publication
User friendly Image metadata annotation tool/workflow for OMERO#
Jens Wendt
Tags: Metadata, Workflow, OMERO
Content type: Forum Post
https://forum.image.sc/t/user-friendly-image-metadata-annotation-tool-workflow-for-omero/87925/1