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
Last meeting: 6th March 2023, 5:00 pm
To gain access to the full meeting minutes, you have to be a registered member of QUAREP-LiMi. Use the “Become a Member” form or write an e-mail to the WG chair.
Major Achievments
Subgroups
Members
Meetings
Major Achievments
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
- 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
Subgroups
- 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
Members
Memberlist WG 7
Meetings
Subgroup Model, 6th meeting, 6th of March 2023
Meeting date
06/03/2023 @ 5:00 PM
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
20th meeting, 20th of February 2023
Meeting date
20/02/2023 @ 5:00 PM
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!
Subgroup Model, 5th meeting, 6th of February 2023
Meeting date
06/02/2023 @ 5:00 PM
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
18th meeting, 21st of November 2022
Meeting date
21/11/2022 @ 5:00 PM
Meeting summary
Caterina reported that all the to-do items from last meeting have been completed. Created a granular task list based on what are tasks identified in each of the Sub-Groups and a link to spreadsheet was added to WG7 mainpage. In addition a proposal was tabled to announce QUAREP-WG7 meetings on Image.sc and it was agreed at the meeting. Ken reported the OME-Meeting on Metadata. Josh’s talk can be found here https://www.openmicroscopy.org/events/ome-community-meeting-2022/ · Great material for advocating about the need of a NG Metadata framework, although no clear definition of storage location. There were much discussion of Nature Methods and Nature Cell Biology request to QUAREP-LiMi to develop a light microscopy checklist for Nature Portfolio. Caterina reported back that we had initial meeting with Rita and Melina to discuss Nature requirements and initial meeting with WG7, 9, 11 and 12 chairs to dicuss next steps. We aim to provide the checklist by Christmas to Nature Methods. Nature is not going to release the data, but something that they will like to work and discuss with their editors.
Subgroup Model, 3rd meeting, 7th of November 2022
Meeting date
07/11/2022 @ 4:00 PM
Meeting summary
- Report back from Mathias and Caterina revision of the Camera Metadata Model based on the feedback from the JOINT CAMERA FEEDBACK GROUP Caterina and Mathias have completed the revision of the DETECTION SYSTEM 2022-10-07_NBO-Q_DETECTOR_v3-00-0_DRAFT_V01 spreadsheet (https://docs.google.com/spreadsheets/d/1KQgAClf4lp90sZ0egUez1h2HYwhvC5VFbaBn1mqvgqE/edit?usp=sharing) Caterina and Mathias have worked at testing LinkML as a framework that we could use to represent the metadata model and would allow the automatic generation of different representations starting from a unique source of truth. · Specifically the advantage of LinkML is that it can use a spreadsheet as the source of truth · The spreadsheet has to be following the schemasheet format (https://linkml.io/schemasheets/) o https://docs.google.com/spreadsheets/d/1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ/edit#gid=55566104 · Mathias and Caterina are testing the schemasheet format to see if it can be used as a source of truth
- Decide on more frequent schedule for follow up meetings · Mathias and Caterina will communicate when the schemasheet version of NBO-Q v3.00_DRAFT is ready to be discussed and presented · David, Mathias, Roland, and Britta will review the 2022-10-07_NBO-Q_DETECTION SYSTEM_v3-00-0_DRAFT_V01 spreadsheet (https://docs.google.com/spreadsheets/d/1KQgAClf4lp90sZ0egUez1h2HYwhvC5VFbaBn1mqvgqE/edit?usp=sharing) so that we can then present it to the CAMERA FEEDBACK GROUP to finalize the request for changes and produce a DRAFT v02 that can be used as a source of truth for implementation
Subgroup Model 2nd Meeting, 5th of October 2022
Meeting date
05/10/2022 @ 4:00 PM
Meeting summary
–Caterina and Mathias are having a series of twice-a-week in-person meetings at UMass Med to produce a revised version of the NBO-Q model Excel Spreadsheet that incorporates all proposals for change that emerged from the series of meetings with Camera Manufacturers (referred to as JOINT CAMERA FEEDBACK GROUP)
The product should be done in 1 month.
–This revised spreadsheet will be used as a starting point for our work as well as to solicit a final round of feedback from the JOINT CAMERA FEEDBACK GROUP.
–We will use LinkML as the framework to represent the metadata model. LinkML core format is YAML but a SPREADSHEET can be used as the core representation from which other representations can be generated.
DECISIONS:
NEXT MEETING ON 11/7/2022 AT 11 am ET and then every 1st Monday after that
LinkML will be tested to support the production of different interlinked representations of the model
