WG 7 – Objectives
Work Group 7 focuses on various aspects of Image Metadata (initially primarily Microscopy Metadata, but also Experimental, Sample, and Analysis Metadata in accordance with REMBI recommendations). These span from defining and continually revising the 4DN-BINA-OME (NBO) Microscopy Metadata model, to facilitating metadata capture through user-friendly tools, to integrating the captured metadata into cloud-ready storage containers such as the newly developed Open Microscopy Environment (OME) Next-Generation File Format (NGFF). To promote the uptake of metadata tools and models, educational material and outreach strategies are also developed.
To carry out these tasks, WG7 is organized into ad-hoc Subgroups (see the “Subgroup” tab below), which are created, paused, or dissolved by WG7 as a whole to accomplish specific goals.
The general meeting serves as a community forum for discussing general topics of interest, reporting on progress achieved within the Subgroups, connecting the dots, and strategic planning.
To participate, please fill in the general QUAREP-LiMi membership form, choose WG7, and, if desired, select a specific Subgroup (see the “Subgroup” tab below) to work on specific tasks.
Still confused? No worries, please join our next working group meetings to know exactly how you can lend a hand.
WG 7 – Meetings
On the 3rd Monday of every other month at 5-6:30 pm UTC +1 . For more details, check the QUAREP-LiMi Calendar.
WG 7 – Co-Chairs
WG 7 - Latest News
We welcome our first member from the United Arab Emirates. Rachid Rezgui of NYU Abu Dhabi joined the Working Groups 1-7, 9, 10 and 13. Change the Quality of Light Microscopy Imaging as member of QUAREP-LiMi join us here.
The WG 1 released its first protocol “Illumination Power and Illumination Stability“. The protocol is featured on
Beside step-by-step instructions, the protocol provides:
- A link to a public database with measurements made by members of our group and to which you can contribute by uploading your own measurements.
- A link to a GitHub repository with scripts to automatize the measurements with some scopes and power meters
- A link to tutorial videos which are available on the QUAREP-LiMi YouTube Channel
We welcome our first member from the Ecuador. William Narvaez joined the Working Groups 1, 3, 5, 9 and 11. Change the Quality of Light Microscopy Imaging as member of QUAREP-LiMi join us here.
Last meeting: 3rd November 2025, 5:00 pm
Global Bioimaging Training Module: Reporting and Reproducibility in Microscopy.
- Reporting and Reproducibility in Microscopy modules are dedicated to image metadata, an essential additional information including dimensions, pixel size, image type, bit depth, and microscope settings, all necessary for extraction of meaningful data from images, quantitative image analysis, and reproducibility of experiments. The training module can be found here.
Protocols.io: Getting started with Micro-Meta App Tutorial
- The tutorial can be found here.
NBO Microscopy Metadata Specifications (full name 4DN–BINA-OME):
- Hammer, Mathias, Maximiliaan Huisman, Alessandro Rigano, Ulrike Boehm, James J. Chambers, Nathalie Gaudreault, Alison J. North, et al. “Towards Community-Driven Metadata Standards for Light Microscopy: Tiered Specifications Extending the OME Model.” Nature Methods, December 3, 2021, 1–14. https://doi.org/10.1038/s41592-021-01327-9. CITE
- Huisman, Maximiliaan, et al. “A perspective on Microscopy Metadata: data provenance and quality control.” arXiv, 24 Oct. 2019, arxiv.org/abs/1910.11370v6.
- Explore
- Provide feedback (How to)
Micro-Meta-App
- Rigano, Alessandro, Shannon Ehmsen, Serkan Utku Öztürk, Joel Ryan, Alexander Balashov, Mathias Hammer, Koray Kirli, et al. “Micro-Meta App: An Interactive Tool for Collecting Microscopy Metadata Based on Community Specifications.” Nature Methods, December 3, 2021, 1–7. https://doi.org/10.1038/s41592-021-01315-z. CITE
- Download
- How to
- Provide feedback
MethodsJ2
- Ryan, Joel, Thomas Pengo, Alex Rigano, Paula Montero Llopis, Michelle S. Itano, Lisa A. Cameron, Guillermo Marqués, Caterina Strambio-De-Castillia, Mark A. Sanders, and Claire M. Brown. “MethodsJ2: A Software Tool to Capture Metadata and Generate Comprehensive Microscopy Methods Text.” Nature Methods, October 15, 2021, 1–3. https://doi.org/10.1038/s41592-021-01290-5. CITE
- Download
- How to
MDEmic (OMERO.mde implementation)
- Kunis, Susanne, Sebastian Hänsch, Christian Schmidt, Frances Wong, Caterina Strambio-De-Castillia, and Stefanie Weidtkamp-Peters. “MDEmic: A Metadata Annotation Tool to Facilitate Management of FAIR Image Data in the Bioimaging Community.” Nature Methods, October 11, 2021, 1–2. https://doi.org/10.1038/s41592-021-01288-z. CITE
- Download
- How to
- GitHub
- Subgroup: Improving the usability of Metadata tools
- Status: SUSPENDED UNTIL FURTHER NOTICE
- Aims: Develop user-friendly tools to input, update, and visualize image metadata.
- Co-leads: Caterina Strambio De Castillia and Roland Nitschke
- Contact information: caterina.strambio@umassmed.edu
- On-going tasks:
- Provide feedback for the design and usability of Micro-Meta App canvases for capturing Laser Scanning Confocal (LSM) and for Spinning Disk Confocal (SDC)
- Cloud storage archive(can be accessed as a member) → here
- Subgroup: Metadata education and outreach
- Status: DISBANDED and MERGED WITH QUAREP-LIMI WG 8 – Education, training, and outreach WG
- Cloud storage archive (can be accessed as a member) → here
- Subgroup: Metadata storage specifications
- Status: SUSPENDED UNTIL FURTHER NOTICE
- Aims: Develop ways and options (e.g., OMERO) to store/manage/retrieve metadata together with image data and, in particular, OME-NGFF
- Co-leads: Guillaume Gay, Ken Ho, and Damir Sudar
- Contact information: dsudar@qitissue.comandkenneth.ho@crick.ac.uk
- On-going tasks:
- Developing Micro-Meta App plugin for OMERO.web
- Integrating Micro-Meta App with OMERO.mde
- OWL/RDF ontology
- Testing JSON-LD as a standard for metadata storage for OME-NGFF
- Cloud storage archive (can be accessed as a member) → here
- Subgroup: Metadata model revision
- Status: ACTIVE
- Aims: Revise the published version of the 4DN-BINA-OME Microscopy Metadata on the basis of feedback from commercial manufacturers and the imaging community.
- Lead: Caterina Strambio De Castillia
- Contact information: caterina.strambio@umassmed.edu
- On-going tasks:
- Implement changes requested for the Detector/Camera model collected during a series of meetings held in Spring 2022 with Camera manufacturers and organized jointly by WG2 and WG7
- Cloud storage location (can be accessed as a member) → here
To join one or more of the groups, you first need to fill in the general QUAREP-LiMi membership form, select WG7, and then, if desired, pick one of the Subgroups.
31st meeting, 21st of October 2024
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Meeting summary
- Report back on work done by members of the WG to align the terminology used in the upcoming WG11 checklist with NBO-Q
- Mandate from the SC to WG7 to generate an NBO-Q landing page.
- The primary target audience for the NBO-Q landing page is QUAREP members.
- The NBO-Q landing page will start by simply delineating the data model and why it is essential to the QUAREP mission. Subsequently, more content, including examples and visualizations, will be added gradually. A group of volunteers were identified to work on moving this project forward. They will present their work during the next meeting.
- In all we do, it is essential to advance together and develop consensus with all members of QUAREP. To this aim, it is crucial to educate all members of QUAREP on what metadata is, how metadata can be represented in machine and human-readable manners, and why organizing metadata in a model is essential.
29th meeting, 17th of June 2024
Meeting date
Meeting summary
Memberlist WG 7