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:
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sanctions Working Groups to form teams that focus on specific technical or outreach topics;
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maintains, disseminates, and teaches best practices, protocols, and software tools; and
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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.
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Working Group 2
24th meeting, 14th of November 2022
Meeting date
14/11/2022 @ 5:00 PM (CET/CEST)
Meeting summary
Thanks a lot to all of you who participated in the lively discussion about our “Detection system behaviour measurements” collection.
We discussed several aspects of the table structure for our measurements and analysis data wich needs to be updated. One major discussion was again about the unique identifier. A solution needs to be found in general for Quarep. Until then we use an intermediate solution with unique identifiers in our excel sheet. Also need to ask the HTS community for their expertise.
Furthermore, Kees reported from his last test runs with the APE quantiflash. His presentation can also be found here on our cloud folder. The other test places will report about their experiences and results in our meeting in February.
23rd meeting, 10th of October 2022
Meeting date
10/10/2022 @ 5:00 PM (CET/CEST)
Meeting summary
We did start our meeting welcoming a new member and refresh a few organisational matters.
This was followed by the report from the WG9 & cochair meeting on Oct 6th:
– More active members are needed for WG9.
– Furthermore, an internal review process was discussed. Please revise and comment on the proposal for the “Internal Review Pipeline”.
The joined group WG2and WG7 is working to consolidate the camera part of the model. The glossary still needs to be finished.
A new organisation of model revision was discussed as well as potential next topics: light sources (maybe two parts: lasers, wide-field illumination), filters, objectives.
We then focused the discussion on AirTable organisation and reporting of measurement and parameters from acquisition and analysis.
As a result of the discussion we agreed to start from excel file in order to define the most important parameter before to transfer all of them in AirTable.
Care should be taken in naming and saving the data in the correct way so that the analysis group can focus on the output parameters and their interpretation.
Acquisition parameters and issue still need to be fixed and all comments should be added to the protocol draft in protocols.io once it is finalised there.
(A QUAREP-LiMi-wide training on ptrotocols.io was planned for beginning of November.)
Still work to do in: testing new samples (marker pen), acquire new images from chroma slide, collect and compare analysis measurements, finalise the transfer of our protocols after the training.
22th meeting, 12th of September 2022
Meeting date
12/09/2022 @ 5:00 PM (CET/CEST)
Meeting summary
The camera metadata (WG2 + 7) group needs to work on a glossary, explaining the terminology used. It was decided that people from the camera subgroup will start working on this glossary. Furthermore, it was decided that we need to start thinking about the next microscope parts, for which the metadata structure and vocabulary can be standardized. Kees reported further on testing of the Quantiflash standardized light source. A continuous (DC) mode should be implemented in addition to the pulsed mode. The standardized light source will be discussed in detail during the November meeting. Personal learning sessions for Protocols.io will be offered to interested members of WG2.
Working Group 3
Working Group 4
56th meeting, 21st of July 2026
Meeting summary
WG04 had a presentation from one of its members, Junqing, from the National Physical Laboratory, UK, on “Dimensionally Traceable 3D Microstructures for Multimodal Microscope Calibration,” followed by a group discussion. The group then discussed the upcoming group elections (for SC, ERB, and OBs); the current co-chairs stated they are willing to remain in their positions, though new nominations are welcome. The group will set up a nomination/election poll.
54th meeting, 21st of April 2026
Meeting date
21/04/2026 @ 5:00 PM (CET/CEST)
Meeting summary
The working group discussed the issue of low attendance at meetings and considered the possibility of increasing visibility through social media channels. This matter will be raised with the Steering Committee (SC) for further guidance.
The group also addressed the development of a new protocol for widefield (WF) and spinning disk (SD) microscopy systems. Attending members agreed to prepare an initial draft covering both modalities. MA will share a link to the first version of the protocol ahead of the next meeting to enable further discussion.
Finally, it was noted that the WG04 abstract submitted for a workshop at ELMI 2026 has been accepted.
53rd meeting, 17th of March 2026
Meeting date
17/03/2026 @ 5:00 PM (CET/CEST)
Meeting summary
The WG was updated by LacJ about the feedback requests from the other WGs and the general news from Quarep‑LiMi. The WG then discussed the abstract outline to be submitted for a workshop at ELMI 2026.
52nd meeting, 17th of February 2026
Meeting date
17/02/2026 @ 5:00 PM (CET/CEST)
Meeting summary
PS updated the group on the latest news from QUAREP‑LiMi. The group discussed the protocol changes to be implemented. AB presented results obtained on different systems from his facility. Based on these findings, new action items were defined. The next meeting is scheduled for March 23.
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
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.
31st meeting, 21st of October 2024
Meeting date
21/10/2024 @ 5:00 PM (CET/CEST)
Meeting summary
The following topics were discussed:
- 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.
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.