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
30th meeting, 8th of May 2023
Meeting date
08/05/2023 @ 5:00 PM (CET/CEST)
Meeting summary
1) First we discussed some general QUAREP-LiMi news:
– report from the WG9 & co-chairs meeting on May 2nd (feedback from general meeting, QUAREP-LiMi Organigram)
2) Second we talked about the preparation of our contribution for ELMI 2023:
– presenters, preparation support team members, dates for preparation meetings, abstract was sent, date for the actual workshop, which setups will be available
3) Third, we review the annual meeting:
– intro session: needs to be improved, idea from WG9: have meeting schemes (Spring: external & outreach, Fall: internal – update about work group progress
– our break out room: comments to follow up (advice about when a detector is OK / not OK; make protocol available)
– main panel (great) & general feedback (general goal of QUAREP needs to be made more clear)
– our survey (short look at the results, need to be looked at closer later)
4) Mathias reported from his EMVA1288 training (will optimize and upload the slides):
– report followed by discussion about how to use the material, how to adapt it to our LiMi needs, we always use EMVA1288 as guidance
5) Last we postponed David’s report again, to the June meeting and agreed on the next steps.
29th meeting, 17th of April 2023
Meeting date
17/04/2023 @ 5:00 PM (CET/CEST)
Meeting summary
Draft versions of the workgroup presentation and survey for the General assembly meeting were shared and suggestions for improvements were given. Discussion topics for the breakout session were given. Mathias’ report from his EMVA1288 training and the update on David MacFadden’s analysis script will be discussed during the meeting in May.
28th meeting, 13th of March 2023
Meeting date
13/03/2023 @ 5:00 PM (CET/CEST)
Meeting summary
- First we discussed some general QUAREP-LiMi news:
- QUAREP-LiMi is now a community partner of image.sc, we potentially need to contribute to the moderating in the future
- there is a community room at ELMI for QUAREP and other imaging communities to do 6 workshops, WG2 member contribution is welcome
- the French MetrologyJ-QC group is very interested in a collaboration with us in WG2, we will invite them to a future WG2 meeting
- WG12 paper is in the review process of Nature methods
- Second we collected ideas on which topics to discuss in the breakout room. It was agreed to especially include open questions and problems: challenge how to measure sensitivity; our strategy of community roll-out; current problems we are facing: UUIDs; data handling, storage, and retrieval. We also collected some potential survey questions. A small team was formed to prepare the breakout room, the short introduction video and questions for a possible survey; all of which will be presented during our next WG2 meeting.
- Third followed the reports from the small group measurement teams: for sample preparation, we now have the text for the marker-pen sample on protocols.io (please check it out). A text is planned for the Chromaslide ramp. MathiasH went to the EMVA1288 certification course. He will report in our next meeting.
27th meeting, 13th of February 2023
Meeting date
13/02/2023 @ 5:00 PM (CET/CEST)
Meeting summary
After first talking about organisational news, we discussed the changes in date and plans for our upcoming QUAREP-LimI general assembly meeting. It is going to be held online on April 26th 2023 3-6PM.
We decided that we want to participate with our own breakout room and formed a small preparation team which will also think about potential questions for a survey. A short video presentation needs to be prepared as well.
Next the small measurement teams reported their results. Team CET focussed on test samples and found the marker pen as bright enough, easy to prepare and use.
Team CET2 focused on the protocol and its usability via protocols.io. There is still a lot of optimization to do (changing the order of the steps, optimizing the run behavior of the protocol).
This discussion was followed by the report from our training session with Emma Ganley from the protocols.io team.
At the end of the meeting we summarized the main next steps: simplify our protocols and the protocols structure, and updated our detection system behavior measurement excel sheet.
The APE measurement reporting session is planned for our June meeting.
26th meeting, 9th of January 2023
Meeting date
09/01/2023 @ 5:00 PM (CET/CEST)
Meeting summary
We used the opportunity of this being the first meeting in 2023 to look back at our achievements, but also challenges, last year.
As a main challenge we identified the motivation and organisation for collecting data and analysing it. This is essential to test and optimise our protocols to be able to finalise and subsequently publish them. We therefore decided to form small groups of 3-4 people doing the measurements together.
In addition, we discussed to have our aims and next steps smaller and more tight, focus on one aim only. This way we will steadily move forward to eventually reach our goal.
Our protocols group gave a brief update on the development of our WG2 protocols in the protocols.io QUAREP-LiMi workspace and informed about the planned training session with Emma Ganley from the protocols.io team.
At the end of the meeting we summarised the main next steps: do measurements in the small groups and contact the protocols.io support team about our needs.
25th meeting, 12th of December 2022
Meeting date
12/12/2022 @ 5:00 PM (CET/CEST)
Meeting summary
We started with a brief report from WG9&co-chairs last meeting, focusing mainly on the next general assembly meeting of QUAREP-LiMi.
In this meeting, we then had a big discussion on Metadata. There is a specific need of finding a good way to collect, name and recover image files.Try to find an agreement on naming the file isn’t universally acceptable. Therefore, the idea is to find a way to recover the most important metadata on acquisition parameters and device settings in a unique format. Omero could be the answer and it requires a list of metadata. In the same direction is also the request from Nature protocol and other editors for publication.
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
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
34th meeting, 10th of December 2024
Meeting date
10/12/2024 @ 4:00 PM (CET/CEST)
Meeting summary
Presentation by Siân Culley (King’s College London): be there!
30th meeting, 12th of March 2024
Meeting date
12/03/2024 @ 4:00 PM (CET/CEST)
Meeting summary
This meeting will be dedicated to a quick review of the RID parameter, a global discussion about the new parameter AS told us about and importantly, the ByLaws document with the need of volunteer candidates for the various positions (SC, EBR, OB).
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.