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
64th meeting, 13th of July 2026
Meeting date
13/07/2026 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organisational matters & News
- Discussion about survey for comparison protocol / recommendations
- Report from ELMI 2026, plan WG2 contributions for 2027 meetings
- Updates on camera model & glossary project, and theory paper
- Summary and next steps
63rd meeting, 8th of June 2026
Meeting date
08/06/2026 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organisational matters & News
- Finalising WG2 contribution to ELMI 2026
- Update on theory paper
- Work on comparison protocol / recomendations
- Summary and next steps
Summary
The 63rd meeting of Working Group 2 focused on preparations for ELMI 2026, where both workshops presented by the group have already sold out. The team reviewed presentation materials for two workshops: one on photoconversion factor measurement led by Kees and Britta, and another on automation protocols presented by Kees. They discussed QR code implementation in presentations and agreed to include both direct protocol links and references to the QUAREP-LiMi website for better accessibility. The group also addressed plans for poster presentations and the status of a theory paper, noting no updates were available from the authors. Additionally, they debated the development of comparison protocols and guidelines, with participants suggesting a survey might help determine community needs before creating formal recommendations.62nd meeting, 11th of May 2026
Meeting date
11/05/2026 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organisational matters & News
- Updates on camera model and glossary project
- WG2 elections
- Updates on: WG2 contribution to ELMI 2026, theory paper
- Work on comparison protocol
- Summary and next steps
Summary
The Working Group 2 meeting focused on election results, project updates, and ELMI preparation. Catalin reported the election results for the new WG2 co-chairs (Valeria Berno, Gert-Jan Bakker, Andre Zeug, Britta Schroth-Diez) and WG2 representatives (SC: Britta Schroth-Diez, ERB: David Grunwald, OB: Andre Zeug). The group discussed the final phase of the camera model and glossary project, which is nearly complete after five years of work. They reviewed plans for ELMI workshops, including two accepted workshop applications, and discussed potential poster abstract submissions for the conference. The meeting also addressed the comparison protocol development, with discussions about light source stability and its impact on measurement results, though the group concluded that light source variation likely wouldn’t affect the current protocol’s results.
61st meeting, 13th of April 2026
Meeting date
13/04/2026 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organisational matters & News
- Preparation for WG2 elections
- Reports from FOM and GerBI-GMB meeting
- Updates on: WG2 contribution to ELMI 2026, theory paper
- Work on comparison protocol
- Summary and next steps
Summary:
After agreeing on the next meeting dates and reporting from the last SC meeting, we discussed the upcoming elections for our WG2 co-chairs and representatives.
This was followed by reports from our very successful WG2 contributions at FOM 2026 and the GerBI-GMB meeting. Next, we talked about our planned contributions for ELMI2026.
The two workshop abstracts were sent in, abstracts for posters still need to be worked on. The theory paper preparation group met at FOM. The next steps planned are to provide a first draft sketch for the paper and a letter to the editor. Both drafts will be presented in the May meeting.
The reminder of the meeting of worked on our comparison protocol. We discussed how to define acceptable variations of the light source used for determining detector parameters. We further discussed how to measure these parameters and how they would link to light source intensity variation. We will continue this discussion in our next meeting.
Working Group 3
Working Group 4
37th meeting, 21st of May 2024
Meeting date
21/05/2024 @ 5:00 PM (CET/CEST)
Meeting summary
WG4 acknowledges the acceptance of the QUAREP by-laws. Judith Lacoste serves as the WG4 Steering Committee (SC) representative, Ileana Micu as the Editorial Review Board (ERB) representative, and Christian Kukat as the Ombuds Board (OB) representative. Also, Maria Azevedo is now co-chair with Aurélien Dauphin. An overarching publication involving WG03, WG04, WG05, and a microscope manufacturer was discussed, and suggestions for WG04 representatives to participate were put forward. An update on the naming convention was provided, and the group discussed what should be included for WG04 datasets. Importantly, WG04 will not meet in June; however, an email containing updates on the naming convention and instructions to test OMERO will be sent. The next WG04 meeting is scheduled for July 16th.
36th meeting, 24th of April 2024
Meeting date
24/04/2024 @ 5:00 PM (CET/CEST)
Meeting summary
A microscope manufacturer is using the QUAREP protocols to provide time-0 measurments before shipping units to its customers. The manufacturer‘s team presented on what seems to be a code implementation issue for the calculation of the reference surface used to calculate the co-registration performance with the tool MetroloJ QC. With the supporting references, they show that the way code is currently written, the 3D reference surface is rendered as a peanut shape instead of an ovoid elongated sphere. As a result of this, the XY and Z co-registration accuracy is not correctly assessed. The authors of MetroloJ_QC will be contacted to present them these findings and ask for feedbacks.
35th meeting, 19th of March 2024
Meeting date
19/03/2024 @ 5:00 PM (CET/CEST)
Meeting summary
WG04 pursues the analyses of 1um beads datasets for color co-registration, comparing different software. There was a discussion regarding measurements of signal to background ratio on aging bead preparations. The group discussed about how detectors settings and metadata can have an impact on the co-registration analysis results. Please note the next WG04 monthly meeting date. It was moved because of QUAREP annual meeting. Lastly, many thanks to the members who agreed to become co-chairs and representatives of WG-04: Maria Azevedo, Aurélien Dauphin, Christian Kukat, Judith Lacoste and Ileana Micu.
34th meeting, 20th of February 2024
Meeting date
20/02/2024 @ 5:00 PM (CET/CEST)
Meeting summary
Today the proposed QUAREP by-laws were presented. WG04 is grateful to those who worked with David Grunwald for the preparation of this impressive document. The by-laws will be submitted for approval during the QUAREP annual meeting next April. In the mean time, WG04 is asking its members to come forward for the following positions in our workgroup: WG04 co-chairs, a WG04 steering committee representative, a WG04 editorial review board representative and a WG04 ombuds board representative. In addition, QUAREP will need to elect 13 persons on the steering committee and 3 persons on the ombuds board. Our organisation just reached 600 members, for sure there will be new people joining on the above committees to make QUAREP better. Please let us know of your interest in the above positions. A big thanks in advance!
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
17th meeting, 19th of September 2022
Meeting date
19/09/2022 @ 5:00 PM (CET/CEST)
Meeting summary
The work of QUAREP-WG7 is done within WG7-Subgroups that have clear goals listed on the WG7 homepage (https://quarep.org/working-groups/wg-7-metadata/).
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.
This organization allows WG7 to carry out several parallel tasks that span from image metadata model specifications, the development of metadata collection tools, the improvement of the metadata storage formats, and the development of educational and training material to onboard biomedical researchers.
DECISIONS:
- The general organization of WG7 is sound, and it will be maintained.
- To leave more time for Subgroup work and reduce time waste, it was decided that we will reduce the frequency of WG7 general meeting while making Subgroup meetings regular and consistent.
- Specifically, the general meeting will be held on the third Monday once every 2 months —> NEXT GENERAL MEETING will be on 11/21/2022 (17:00 CEST / 11:00 EST)
- The same slot will be utilized as needed by the subgroups. For example, the next WG7-Subgroup 2 meeting will take place on the 17th of October (17:00 CEST / 11:00 EST).
- At the same time, it is essential to improve communication and progress management to make sure people have a clear idea of what is happening, and how they can contribute.
- To facilitate the division of labor and communication, we will create granular task lists in Excel and link the list from the WG7 homepage (https://nextcloud.quarep.org/index.php/s/DgJBQnjg3jSMgx8). The list will be bae on the tasks emerging from Sub-Group meetings, will provide precise instructions, and include clear due dates (e.g. Subgroup 1: TASK = provide feedback on Micro-Meta App Confocal canvases; DUE=10/17/2022)
16th meeting, 18th of July 2022
Meeting date
18/07/2022 @ 5:00 PM (CET/CEST)
Meeting summary
Despite considerable progress (publications, collaborations with other working groups, feedback from manufacturers, further development of metadata collection tools, educational material, outreach, etc.), participation has been waning.
To address this issue, we discussed the following topics:
1) What can we do to improve motivation and participation?
2) What should be our goals for the upcoming year?
The discussion was very animated and participated. Several constructive suggestions were made. In summary:
1) Having subgroups allows to achieve tasks, but it can be very confusing. It is important to improve the organization of the work and communication to members on what needs to be done and what is done:
– agreed upon, small, and achievable tasks
– clear schedule (always advertised on the QUAREP calendar)
– report back consistency on goals and progress
2) It is important to shift focus from Microscopy Metadata to Experimental/Sample Metadata capture. Would it make sense for WG7 to be involved in developing standards around these topics?
3) It is important to develop guidelines but for work to be successful and productive, WG7 has to be involved with developers to produce tools that implement the guidelines and bring them to life for imaging scientists.
Next steps:
– The August meeting is canceled. See you back in September
– In September, all Subgroups will have a meeting to organize next year’s schedule (regular or not?) goals and activities.
– Co-Chairs will meet to decide whether a survey to collect feedback on future goals is needed for all WG7 members (even those that do not participate in sub-groups).
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
46th meeting, 03rd March 2026
Meeting date
05/03/2026 @ 11:03 AM (CET/CEST)
Meeting summary
Decide on next chair (Chloe’s torch bearer)
Ayse: Discuss her idea of IA she is working on
Define what depends on application means.
QUAREP-endorsed MicCheck?
Review the modalities we already discussed to ensure we are still ok with them.