FAIR High Content Screening in Bioimaging
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BiBTeXThe Minimum Information for High Content Screening Microscopy Experiments (MIHCSME) is a metadata model and reusable tabular template for sharing and integrating high content imaging data. It has been developed by combining the ISA (Investigations, Studies, Assays) metadata standard with a semantically enriched instantiation of REMBI (Recommended Metadata for Biological Images). The tabular template provides an easy-to-use practical implementation of REMBI, specifically for High Content Screening (HCS) data. In addition, ISA compliance enables broader integration with other types of experimental data, paving the way for visual omics and multi-Omics integration. We show the utility of MIHCSME for 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 Findable, Accessible, Interoperable and Reusable (FAIR) bioimaging data throughout the Netherlands Bioimaging network.
SEEK ID: https://fairdomhub.org/publications/816
DOI: 10.1038/s41597-023-02367-w
Projects: NL-Bioimaging FAIR Metadata Templates
Publication type: Journal Article
Journal: Scientific Data
Book Title: Scientific Data
Publisher: Springer Science and Business Media LLC
Citation: Sci Data 10(1):462.
Date Published: 17th Jul 2023
Registered Mode: by DOI
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Created: 10th Aug 2026 at 08:14
Last updated: 10th Aug 2026 at 08:16
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Projects: NL-Bioimaging FAIR Metadata Templates
Institutions: University of Leiden
https://orcid.org/0000-0002-3704-3675
Projects: NL-Bioimaging FAIR Metadata Templates
Institutions: University of Leiden
https://orcid.org/0000-0002-0615-9616
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
NL-BioImaging AM is a distributed research infrastructure aimed at promoting progress in the most cutting edge microscopy technologies and providing open access to these technologies to a broad community of academic and industrial users. All Netherlands bio(medical) microscopy centers participate.
FAIR (Findable Accessible, Interoperable and Reusable) data management is a challenge for the optical microscopy community due to a high diversity in participating research fields and methodologies, ...
Projects: NL-Bioimaging FAIR Metadata Templates
Web page: http://eurobioimaging.nl/
This project collects and maintains minimum information metadata templates designed and used in the National NL-Bioimaging initiative. The templates are based on the REMBI standards and contribute to FAIR bioimaging data in the Netherlands, together with data management in the OMERO database.
Programme: NL-Bioimaging: FAIR-DM
Public web page: http://eurobioimaging.nl/
An example template for screen published in IDR (idr0002, screenA).
Access Level: Published
https://idr.openmicroscopy.org/search/?key=name&value=idr0002&resource=container&operator=equals
An example template for screen published in IDR (idr0022, screenA).
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
An example template for screen published in IDR (idr0022, screenB).
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
An example of MIHCSME describing live cell imaging HepG2 -GFP reporter line.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
