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.
We welcome our first member from the China. Xiaoming Li from ShanghaiTech University, joined the Working Groups 1 to 11. Change the Quality of Light Microscopy Imaging as member of QUAREP-LiMi join us here.
Upcoming meeting: 16th December 2024, 5:00 pm
Last meeting: 21st October 2024, 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
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- 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
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- How to
- GitHub
- 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
- 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
- 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
- Subgroup: Metadata model revision
- 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
Memberlist WG 7
31st meeting, 21st of October 2024
Meeting date
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.