Working Group 1
Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy
The Consortium for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi), formed by the global community of practitioners, researchers, developers, service providers, funders, publishers, policy makers and industry related to the use of light microscopy, is committed to democratizing access to quantitative and reproducible light microscopy and the data generated by it.
Our mission is to provide a comprehensive set of community-agreed guidelines, protocols, automation procedures and other resources aimed at improving quality control, quality assurance, and instrument/method calibration. The stakeholders advocate for the use of the highest level of reproducibility for data generated by light microscopy methods in scientific research and biotechnology applications. In support of achieving its mission, QUAREP-LiMi:
-
sanctions Working Groups to form teams that focus on specific technical or outreach topics;
-
maintains, disseminates, and teaches best practices, protocols, and software tools; and
-
collaborates with providers of reference materials or instrumentation or other tools that enable the easy implementation of best practices at the community level.
We came together in our first online Web meeting on the 28th of April, 2020, with about 50 attendees. By now (24st of April 2024), the network has grown to 620 people from 41 countries worldwide. We have members from academia (research labs, core facilities), national microscopy communities, companies involved in the microscopy business, organizations or institutions related to standardization on a national or international level, and scientific publishers and observers from funding agencies (see the graph below and on the member page for an overview).
Ten working groups (WGs) were established in the 2nd General Meeting on the 9th of July 2020 to bring our common aims quickly forward. Our web page gives an overview of QUAREP-LiMi’s work. In the 3rd General Meeting, WG 11 “Microscopy Publication Standards” and later WGs 12 “Image Visualization and Analysis” and 13 “Phototoxicity” were established. WG 14 “Environment” and 15 “FLIM” are in the process of being established, and WG 8 is restructured to work on “Education, Training and Outreach”.
QUAREP-LiMi operates a NextCloud and an OMERO server, serving as a centralized repository and exchange point for our collective work. These platforms facilitate collaboration and data sharing among our members.
QUAREP-LiMi is absolutely open to new members, and we are looking forward to your contribution. If you are interested in joining our initiative, please fill out our membership form. Use our form for changing your working group (WG) or joining a new WG. For any further questions, please contact us.
{{ecs-article}}
Working Group 2
54th meeting, 8th of September 2025
Meeting date
08/09/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- Update on NBO-Q camera model & glossary
- Updates after the summer break (paper, automation…)
- Decide on next priorities
The meeting welcomed new member Kemp Watson and covered organizational updates from the steering committee, including various project developments and upcoming meetings scheduled for October and November. The working group discussed their focus on detection system performance, including camera models and standardized terminology for microscopy systems, while also addressing the progress of a manuscript related to protocol series. The team reviewed developments of the Nikon toolkit and discussed next steps for their project, including the sequential completion of camera work before moving to other detector types.
53rd meeting, 23rd of June 2025
Meeting date
23/06/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- Report from ELMI 2025
- Update on NBO-Q camera model & glossary
- Report from paper working group
- Next steps
The meeting opened with updates from SC and WG7 meetings, including a report from the NBO-Q camera model and glossary project.
Encouraging news was provided about Nature Publishing Group implementing reproducibility checklists inspired by QUAREP-LiMi’s work. These were mentioned in three recent editorials across major journals. However, concerns were raised as essential information is still missing. A broader conversation on FAIR data sharing followed, highlighting the need to better recognize the cost and effort of data acquisition. QUAREP is encouraged to engage more actively in this direction.
Feedback from ELMI 2025 was very positive—QUAREP-led workshops were well attended and sparked interest among participants, many of whom were new to the initiative. This encouraged us to strengthen our outreach efforts for future international meetings, including next year’s ELMI.
Finally, the paper working group is drafting a publication outlining the foundation of the WG2 protocols. While initial writing has begun, broader input is needed. Future publishing plans for the automation tool and data samples will depend on the setup of OMERO and collaboration with companies.
52nd meeting, 12th of May 2025
Meeting date
12/05/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- QUAREP-LiMi ELMI 2025 workshop contribution
- Report from OMERO subgroup meeting
- Update on NBO-Q camera model & glossary
- Report from paper working group
- Next steps
Summary
We started the meeting with discussing our summer meeting scenario. Due to a public holiday and ELMI 2025, we decided to shift our June meeting to June 23rd. In addition, we decided to skip the meetings in July and August to have time for finishing the camera model and glossary, work on the paper, and have time for vacation. We decided to start again with the regular meeting schedule on September 8th.
This summer meeting organisation was followed by a report from the May steering committee meeting. One great news for WG2 was that the SC endorsed the terminology “dexel” for the detector element versus “pixel” as picture element. Next, we briefly discussed the current status of our ELMI workshop preparation.
This was followed by a report from the QUAREP-LiMi OMERO subgroup meeting. A naming convention was introduced by that subgroup, which everybody needs to follow. We discussed how to implement our spreadsheet terms and how to best automate the upload to OMERO. The WG2 co-chairs will look over tags and naming structure for WG2.
This discussion was followed by an update from the NBO-Q camera model and glossary group. The stakeholder group finished working on the hardware part and will now continue with the settings. The plan is to be finished by the end of this summer.
The WG2 paper working group reported from their first meeting where they summarised paper-related content from our past meeting minutes.
We finalised the meeting with summarising the next steps: finalise the NBO-Q camera model and glossary, work on our paper and collect data for it, support WG7 in their work to calibration metadata, and generalise the automation of our WG2 protocols collection to have it eventually working on all microscopy platforms.
51st meeting, 14th of April 2025
Meeting date
14/04/2025 @ 5:00 PM (CET/CEST)
Meeting summary
After discussing possible scenarios for our WG2 work during summer, we reported from the SC meeting on April 1st. This was followed by a detailed report from the Annual QUAREP-LiMi Meeting that took place April 10th.
The ELMI contribution preparation team reported the submission of three workshop abstracts. Approval was expected to be highly likely (by now all our submitted workshops have been accepted).
The NBO-Q camera glossary team could report that the hardware part is finished! Next, the settings part will be tackled, but is not expected to take that long. The rest of the meeting we spend on collecting topics for WG2 to work on in the future: automation for our WG2 protocols, paper to accompany our WG2 protocol collection, collect data for it, NBO-Q model update for point detectors, amongst others. For each of these topics we need to find people to take the lead and define respective time lines.
50th meeting, 10th of March 2025
Meeting date
10/03/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda points
- Organizational matters and News
- Report from the Annual QUAREP-LiMi meeting
- ELMI 2025 workshop contribution
- Update on NBO-Q camera model & glossary
- Next steps
Summary
This meeting was a bit of a house-keeping meeting. After the report from the March SC meeting we briefly discusses our planned contributions to the Annual QUAREP-LiMi meeting. This was followed by setting up a time line and preparation group for organising our contribution to ELMI2025. Next, we had a quick update on the current status of our NBO-Q camera model and glossary project. We closed the meeting with discussing the next projects we need to tackle. We will first focus on preparing our paper and organising collection of data. We will also have to revisit our long-term goals as next big projects.49th meeting, 10th of February 2025
Meeting date
10/02/2025 @ 5:00 PM (CET/CEST)
Meeting summary
This was our first meeting since the publication of our WG2 Protocols collection. Therefore, our main focus was to discuss the next steps for our work.
We agreed on a key concern: how to collect data now that the protocol is available, and how we can assist users in automating the data collection process for use with the analysis tool. We agreed to use OMERO as our main tool. However, this will require significant work. We need to have an easy way to upload data to the OMERO server. Secondly, we need to determine the metadata necessary to support the main detector parameters that can be analysed using our published protocol tools.
Secondly, we got an update on the progress of the Camera Glossary and Model work. The hardware part is almost done. This will be followed by working on the settings part.
Finally, we decided to use the exciting possibility to present our Protocols collection by offering one or two workshops in the community room during the ELMI meeting in June 2025 in Heidelberg.
Working Group 3
Working Group 4
Working Group 5
62st meeting, 9th of July 2026
Meeting date
09/07/2026 @ 3:30 PM (CET/CEST)
Meeting summary
Meeting covered volunteers for elected posts, ELMI feedback, OMERO upload catch up and data collected so far to determine best bead size for ISM based systems. Lastly, a presentation from an intern at the French metrology group detailing software development for identifying aberrant PSFs.
Working Group 6
Working Group 7
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
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.
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.
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.
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.
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
Working Group 8
14th meeting, 23rd of April 2025
Meeting date
23/04/2025 @ 4:00 PM (CET/CEST)
Meeting summary
Summary (topics discussed): Presented and discussed objectives and survey, provided feedback from GerBI, who saw the survey. Sylvia and Gaby showed the latest changes made to the survey. Asked for more contributions (links were shared again). Angela suggested also we have someone more expert on surveys go through the questions (especially making it quantifiable through better structured Likert scales?).
Once this is sorted the Gaby sends a preview of the survey to all QUAREP for final feedback, on the spirit of opening to all community before going public with results.
We ten plan for a date for releasing if and when there is consensus.
Ask also to vote on whether we can/should ask for email (as optional, never mandatory!).
Working Group 9
Working Group 10
41st meeting, 09th of December 2025
Meeting date
09/12/2025 @ 4:00 PM (CET/CEST)
Meeting summary
Discussion about dexel definition work between WG2, WG7 and WG10;
Raw image definition paper V0.8: What‘s new? What remins to be done? Proofreading and assignment of tasks. Target publication date, timeline and help (all)
40th meeting, 14th of October 2025
Meeting date
14/10/2025 @ 4:00 PM (CET/CEST)
Meeting summary
Discussion about Pixel vs Dexel definitions. Validation of the document.
Presentation by John Oreopoulos (Andor) about methods to measure internal scan head background levels, discussions.
Working Group 11
40th meeting, 22nd of May 2025
Meeting date
22/05/2025 @ 5:00 PM (CET/CEST)
Meeting summary
1-During the last meeting, you expressed your wish to publish the bare minimal list as a standalone document instead of the comprehensive manuscript we were initially envisioning. The main concerns we have are figuring out the type of journal that accepts this format/content and the fact that there are at least 3 publications providing guidelines/checklists for methods reporting.
2-The second action item was to organize the live document that we created a long time ago in which we determined what was level 1 (required), 2 (depends on the application), 3 (nice to have) to build a logic tree for biologists to generate the appropriate checklist depending on the experiment they did.