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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

The Light Microscopy Metadata Model (LiMi-Model): Enabling the Generation and Sharing of Reproducible, Community-Harmonized FAIR Bioimage Data (QUAREP-LiMi WG7-Matadata) ELMI Workshop
🎤 Caterina Strambio De Castillia

Presenter(s): Caterina Strambio-De-Castillia *1

*- the workshop was presented on behalf of QUAREP-LiMi WG7-Metadata.

1. Program in Molecular Medicine, UMass Chan Medical School

A major output of QUAREP-LiMi is the Light-Microscopy Metadata Model (LiMi-Model) [1, 2], developed by the QUAREP-LiMi Metadata Working Group (WG7) in collaboration with BioImaging North America, the 4D Nucleome consortium and OME. The LiMi-Model was designed to harmonize the description of light microscopy hardware, acquisition settings, and quality-control metrics in order to enhance image quality and reproducibility, and to fulfill the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Specifically, the LiMi-Model aims to: (1) promote the harmonized generation and pre-publication management of image datasets that are FAIR by design; (2) facilitate the deposition of FAIR microscopy datasets to public image data repositories; (3) facilitate data reuse and the extraction of quantitative information from image data using advanced bioimage analysis techniques, including AI/ML; and (4) define the light microscopy implementation of the Image Acquisition module of the Recommended Metadata for Biological Images (REMBI) guidelines [3].

The workshop will open with a general introduction to the purpose and scope of the LiMi-Model, situating it within the broader landscape of community initiatives. These include the recently published minimal reporting recommendations for light microscopy [4], REMBI, the International Standards Organization, imaging modality ontologies (such as FBbi and EDAM-bioimaging), and an emerging vision for next-generation metadata schema definition languages. This will be followed by a presentation of the LiMi-Model website [1] and interactive LiMi-Model Viewer, a tool designed to help community members navigate and understand the content of the model. The workshop will conclude with an overview of the LiMi-Model’s governance structure and an explanation of how community members can engage with and contribute to its ongoing development. As a concrete example of this process, the workshop will introduce the recent Camera Module revision, conducted in partnership with camera manufacturers whose outcomes will also be presented in a related poster presented in collaboration with QUAREP-WG2.

The formal presentations will be followed by an open discussion in which attendees are encouraged to provide feedback and help shape the future direction of the LiMi-Model.

[1] https://quarep.org/working-groups/wg-7-metadata/limi-model

[2] https://doi.org/10.1038/s41592-021-01327-9

[3] https://doi.org/10.1038/s41592-021-01166-8

[4] https://doi.org/10.1083/jcb.202601032

Join the QUAREP-LiMi Workshops at ELMI

We are pleased to announce that the QUAREP-LiMi consortium will be presenting five specialized workshops at the upcoming European Light Microscopy Institute (ELMI) meeting. Our sessions are designed to provide researchers with frameworks for improving image quality, ensuring data reproducibility, and implementing rigorous quality control standards in microscopy. The workshops will cover five critical pillars of instrument characterization:

  1. The QUAREP-LiMi Tool Kit (WGs 1 & 2):

    Discover how to streamline periodic quality assessments. We will present the latest developments in the Tool Kit, including user-friendly software tools for illumination power and stability (compatible with Nikon and Zeiss), as well as its data browser for long-term performance monitoring.

  2. Detector Performance & Photon Characterization (WG2):

    Learn how to transition from "arbitrary digital units" (ADU) to actual photon counts using the Photon Transfer Curve (PTC) method. We will demonstrate protocols for characterizing photon conversion factors, read noise, and dynamic range for both point and area detectors.

  3. Assessing the co-registration accuracy of a microscope (WG4):

    Chromatic aberration is a major source of spatial error in multi‑colour fluorescence microscopy. This workshop will show practical hints and tips to perform routine co‑registration measurement and analysis.

  4. Point Spread Function (PSF) Analysis (WG5):

    This workshop provides a practical guide to PSF measurement—from beads slide preparation and image acquisition to analysis using open-source tools and integration with OMERO for longitudinal monitoring.

  5. The Light-Microscopy Metadata Model (LiMi-Model, WG7):

    In collaboration with BioImaging North America, 4D Nucleome, and OME, we will introduce the LiMi-Model. This framework aims to harmonize the description of hardware and acquisition settings to ensure datasets are FAIR (Findable, Accessible, Interoperable, and Reusable) by design.
We look forward to engaging with you and hearing your feedback during these sessions!

QUAREP-LiMi welcomes our first member from Nigeria

We warmly welcome our first member from Nigeria, Dr Olubunmi Ayobami Balogun, from the University of Ibadan who just joined Working Group 1, 4 and 12.

 

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.

40th meeting, 9th of March 2026

Meeting date

09/03/2026 @ 5:00 PM (CET/CEST)

Meeting summary

Topics: 1) WG7 Participation in the ELMI Meeting ———————————- It was agreed that WG7 will submit an abstract for a community workshop at ELMI, focused on the LiMi-Model. Also, it was decided that WG7 will support WG2 on a workshop or poster about the LiMi-Model_Camera revision process and outcome. 2) Discussion on the LiMi-Model website and LiMi-Model Viewer —————————————————— Participants were requested to provide feedback on the following three topics (please find details in the minutes document): 1) The LiMi-Model Viewer functionality 2) The LiMi-Model Viewer legend 3) The BP document 3) Content of the ELMI LiMi-Model Workshop ————————————– This workshop will serve as the first major outreach effort for the LiMi-Model, covering its purpose, governance structure, and the ways in which community members can engage and contribute. To provide a broader context, the workshop will open with an introductory presentation situating the LiMi-Model within the wider landscape of community metadata initiatives, including REMBI, imaging modality ontologies (such as FBbi and EDAM), and Next Generation Metadata schema definition languages. This aims to bring greater clarity to the range of ongoing efforts in the field. The workshop will cover the following topics: – Presentation of the LiMi-Model website – Presentation of the model visualisation (prepared by Antony) – Overview of model governance and contribution pathways

Meeting documentation

39th meeting, 19th of January 2026

Meeting date

19/01/2026 @ 5:00 AM (CET/CEST)

Meeting summary

WG7 met to kick off 2026 with introductions, including a few new faces, and a round where everyone shared their wishes for the year ahead. The group caught up on ongoing work around light microscopy metadata, including LiMi-Model, REMBI alignment, and links to efforts beyond bioimaging. We discussed updates on repositories, community coordination, and the fact that several new full-time positions have now been funded to work specifically on metadata extensibility. Looking ahead, the group plans a future presentation on the Czech national strategy for metadata, and agreed on a handful of practical next steps to keep the different efforts better aligned.

Meeting documentation

38th meeting, 17th of November 2025

Meeting date

03/11/2025 @ 5:00 PM (CET/CEST)

Meeting summary

The following decisions were made regarding the revision of the QC/Performance Extension of the NBO-Q (aka LiMi Model) DECISION 1: “QC/QC Run” shall be fused with “QC/QA assay” DECISION 2: DateTime and ProtocolUsed fields will be added to both Sample and Experiment NEXT STEP: CONSENSUS: invite people from QUAREP WG12 and BINA Informatics WG to present about the current state of the art. Ask them to provide a representative who will be available to present at our next meeting.

Meeting documentation

37th meeting, 15th of September 2025

Meeting date

15/09/2025 @ 5:00 PM (CET/CEST)

Meeting summary

Discussion about the new name for the NBO-Q model: WG7 will present the three finalist names to the SC and present the pros and cons of each of the three names. At the same time, a vote was held to determine the preferred name of WG7. 2) Update on the status of the NBO-Q webpage: Anthony presented progress towards an interactive viewer of the NBO-Q to be used for the website. 3) REMBI-DCAT-AP presentation: Marek Cebecauer presented work performed by the Czech Core Metadata Model (CCMM) initiative to build a DCAT-based REMBI schema. 4) Announcement of the successful funding of the Imaging-Persistent Hardware Descriptor (PHD) project to assign persistent identifiers to individual microscopes and their hardware descriptors.

Meeting documentation

36h meeting, 16th of June 2025

Meeting date

16/06/2025 @ 5:00 PM (CET/CEST)

Meeting summary

We had an extended conversation about the naming of the NBO-Q model, eliminating some of the previous suggestions and adding a few new which will be sent out to WG7 again for further voting. We also looked at the status of the website update and reported on discussions from ELMI.

Meeting documentation

35th meeting, 5th of May 2025

Meeting date

05/05/2025 @ 5:00 PM (CET/CEST)

Meeting summary

Worked on aligning attributes from the “MetricDataset”, “MetricsOutput” and “KeyMeasurements” classes of microscopemetrics-schema with NBO-Q NEXT STEPS:

Discuss with Julio ML about the mapping and questions that were put forth during this meeting

Meeting documentation

34rd meeting, 23rd of April 2025

Meeting date

23/04/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 18th meeting, 7th of April 2025

Meeting date

07/04/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 17th meeting, 3rd of March 2023

Meeting date

03/03/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

33rd meeting, 17th of February 2025

Meeting date

17/02/2025 @ 5:00 PM (CET/CEST)

Meeting summary

The meeting covered updates on France BioImaging’s metadata efforts, including OMERO.quay beta testing, buffer server deployment, and authentication improvements. WG10 discussed defining “raw” images and their metadata requirements, emphasizing the need for clarity on file formats. The website report highlighted the need for better organization and visibility of resources, with a proposal to create a landing page and potentially rebrand NBO-Q. Discussions on synonyms and profiles addressed term mapping challenges and possible alias extensions. Additional topics included a McGill student project porting NBO-Q to LinkML and preparations for an ISO discussion at OME2025. The next meeting date requires rescheduling due to Easter.

Meeting documentation

Memberlist WG 7