WG 7 – Metadata

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WG 7 – Objectives

The Work Group 7 focuses on various aspects of Image Metadata (initially primarily Microscopy Metadata but also Sample and Analysis Metadata). 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 on these tasks, WG7 is organized into four Subgroups (see “Subgroup” tab below), each of which carries out specific objectives. These subgroups are created, paused, or dissolved on a needs basis as agreed by the WG7 as a whole.

The general meeting serves as a space for reporting back on the progress that has been achieved within the Subgroups, connecting the dots, strategic planning, and general discussions.

The Subgroups (see “Subgroup” tab below) identify specific tasks to be carried out to move our work forward. To participate, please first fill in the general QUAREP-LiMi membership form and then enter your name here. Still confused? No worries, we have a specific list of tasks that you can check out to know exactly how you can lend a hand.

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:

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: 5th May 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 4DNBINA-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/s41592-021-01327-9CITE
    • 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

  • 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/s41592-021-01290-5CITE
    • 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-zCITE
    • Download
    • How to
    • GitHub
  1. Subgroup: Improving the usability of Metadata tools
    • 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 location (can be accessed as a member) → here
  2. Subgroup: Metadata education and outreach
    • Aims: Develop guidelines and educational material for users to understand and record image metadata
    • Co-leads: Nathalie Gaudreault and Aastha Mathur
    • Contact information: aastha.mathur@eurobioimaging.eu
    • Cloud storage location (can be accessed as a member) → here
  3. Subgroup: Metadata storage specifications
    • 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 location (can be accessed as a member) → here
  4. Subgroup: Metadata model revision

To join one or more of the groups, you need first to become a member of QUAREP-LiMi here, where you can select WG7 as one of the Work Groups you want to participate in. Once you have access to the cloud server, you can enter your name in this spreadsheet to join the respective subgroups.

30th meeting, 19th of August 2024

Meeting date

19/08/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 14th meeting, 8th of July 2024

Meeting date

08/07/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

29th meeting, 17th of June 2024

Meeting date

17/06/2024 @ 5:00 PM (CET/CEST)

Meeting summary

Julio presented an extension to OMERO for tracking metrology data. During the discussion next steps were discussed which included attending WGs 3, 4, and 5 and presenting the work in order to align the metadata schema. There were also extended discussions about recent events, e.g., at OME2024 and ELMI2024.

Meeting documentation

Subgroup Model, 13th meeting, 6th of May 2024

Meeting date

06/05/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

28th meeting, 15th of April 2024

Meeting date

15/04/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

Subgroup Storage, 15th meeting, 26th of March 2024

Meeting date

26/03/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 12th meeting, 4th of March 2024

Meeting date

04/03/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

27th meeting, 19th of February 2024

Meeting date

19/02/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 11th meeting, 5th of February 2024

Meeting date

05/02/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

Subgroup Storage, 14th meeting, 30th of January 2024

Meeting date

30/01/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

Memberlist WG 7