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
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.