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WG 7 – Metadata

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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

 

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):

  • Micro-Meta-App

  • 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
  • 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:
      • Developing Micro-Meta App plugin for OMERO.web
      • Integrating Micro-Meta App with OMERO.mde
      • OWL/RDF ontology
      • Testing LinkML as a standard for metadata storage for OME-NGFF
    • 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.

24th meeting, 26th of June 2023

Meeting date

26/06/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

23rd meeting, 7th of June 2023

Meeting date

07/06/2023 @ 3:00 PM (CET/CEST)

Meeting documentation

22nd meeting, 15th of May 2023

Meeting date

15/05/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

Subgroup Capture Tools, 7th meeting, 19th of April 2023

Meeting date

19/04/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 7th meeting, 3rd of April 2023

Meeting date

03/04/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

21st meeting, 20th of March 2023

Meeting date

20/03/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 6th meeting, 6th of March 2023

Meeting date

06/03/2023 @ 5:00 PM (CET/CEST)

Meeting summary

The main topic of the meeting was the discussion of the NBO-Q Microscopy Metadata Map. The Map aims to facilitate the distribution of responsibilities among WGs regarding the documentation of Microscope Hardware, Acquisition Settings, and Quality Control procedures. Caterina presented the schema she prepared and received feedback. As a result of the feedback, the map was updated. The current version of the map can be found here: https://nextcloud.quarep.org/index.php/s/E3AKjNMbWgXDN3B

Meeting documentation

Subgroup Storage, 13th meeting, 21st of February 2022

Meeting date

21/02/2023 @ 4:00 PM (CET/CEST)

Meeting documentation

20th meeting, 20th of February 2023

Meeting date

20/02/2023 @ 5:00 PM (CET/CEST)

Meeting summary

During the meeting we discussed the following items: 1) Next meeting will be held on March 20th 2023 and then we will continue every two months on the 3rd Monday. 2) Reminders will be sent 1 month, 1 week, 1 day, and 1 hour before each meeting. 3) The work of the WG will continue to concentrate on revising the 4DN-BINA-OME Microscopy Metadata Model and, as much as possible, will attempt to maintain compatibility with REMBI as a high-level set of recommendations. 4) WG7 works to collect the requirements of all WGs and create a consensus that incorporates the metadata requirements of all other WGs. As such WG7 works as an underlying platform on which all other WGs can build. It is important that we do a better job to explain to the QUAREP’s community that our work should be conceived as spanning across multiple WGs. 5) We need a general map of all components of the model, how they relate to each other, and which is the responsibility of which WGs 6) WG7 would like to have time during the annual meeting to discuss with everyone on this!

Meeting documentation

Subgroup Model, 5th meeting, 6th of February 2023

Meeting date

06/02/2023 @ 5:00 PM (CET/CEST)

Meeting summary

Discussion concerned primarily on review of current model revision activities and how to best handle the proposal/review/acceptance/implementation process when faced with the need to revise the NBO-Q model. Consensus: At the moment we are volunteer-driven and changes will have to be done on the basis of individuals taking the lead, driving a revision, putting together a revision and then submitting to the rest of the group for review, acceptance and implementation In this context, when a team of individuals is putting lots of work in making changes and they request feedback it would be great if people would take into account the amount of work that was done and be respectful Going forward we will need a formal method to propose/review/accept/implement changes to the model as the current model is not going to work for developers [a rough estimate would indicate that10000 hours of development are going to be needed for each model request for-change) RE: Camera model revision to increase efficiency concentrate on producing minimal description for each field and in a second round work on a more extensive glossary

Meeting documentation

Memberlist WG 7