WG 7 – Objectives
Work Group 7 focuses on Image Metadata (initially Microscopy Metadata, but increasingly Experimental, Sample, and Analysis Metadata as well, in line with REMBI recommendations).
Our work spans defining, updating, extending, and maintaining the Light Microscopy Model (published in Nature Methods) of metadata specifications, formalizing Best Practices for the LiMi-Model revision process, building user-friendly tools for metadata capture (such as Micro-Meta App, MethodsJ2 and MDEmic), and integrating captured metadata into cloud-ready storage containers such as the Open Microscopy Environment (OME) Next-Generation File Format (NGFF).
The QUAREP-LiMi Steering Committee has formally endorsed the LiMi-Model, affirming its status as one of the organization’s major outputs. Building on this endorsement, WG7 recently launched the LiMi-Model website, which includes the LiMi-Model Viewer, a user-friendly tool for easily navigating the model.
As an essential part of this work, we are developing and promoting the use of the Next Generation Metadata Framework (NGMF), a LinkML-based, community-driven schema definition language designed to keep metadata interoperable while remaining easy to extend and maintain.
Alongside these efforts, we collaborate with WG 8 – Education, training and outreach, to produce educational material and outreach strategies that promote the adoption of the LiMi-Model and its related tools.
To carry out this work, WG7 organizes into ad-hoc Subgroups (see the “Subgroup” tab below), which are created, paused, or dissolved as needed to accomplish specific goals. Our general meetings serve as a community forum for discussing topics of broad interest, reporting on Subgroup progress, and coordinating strategy across the group.
To get involved, complete the general QUAREP-LiMi membership form, select WG7, and, if you’d like, choose a specific Subgroup (see the “Subgroup” tab below) to work on.
Still not sure where to start? Join one of our upcoming working group meetings — we’re happy to help you find the right fit.
WG 7 – Meetings
On the 3rd Monday of every other month at 5-6:30 pm UTC +1.
Last meeting: 9th March 2026, 5:00 pm
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.
Last meeting: 9th March 2026, 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.
Light Microscopy Model (LiMi-Model) of metadata specifications (formerly known as 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 with the LiMi-Model Viewer
- GitHub
- 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
ACTIVE
- Subgroup 4: Metadata model revision
- Status: ACTIVE
- Aims: Revise the published version of the LiMi-Model of metadata specifications on the basis of feedback from commercial manufacturers and the imaging community.
- Lead: Caterina Strambio De Castillia
- Contact information: caterina.strambio@umassmed.edu
- Ongoing 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
- Changing the overall structure and content of the LiMi-Model Calibration and Performance extension.
- Cloud storage location (can be accessed as a member) → here
SUSPENDED
- Subgroup 1: 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
- Ongoing 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 2: Metadata education and outreach
- MERGED WITH QUAREP-LIMI WG 8 – Education, training, and outreach WG
- Cloud storage archive (can be accessed as a member) → here
- Subgroup 3: 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
- Ongoing tasks:
- Cloud storage archive (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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- 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
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Memberlist WG 7