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
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
49th meeting, 16th of September 2025
Meeting date
16/09/2025 @ 5:00 PM (CET/CEST)
Meeting summary
LacJ updated the group on the latest news from QUAREP-LiMi. The group then discussed the results and the discussion section of the protocol, and it was agreed to include the data obtained using MetroloJ_QC, where the experimental distance is normalized to the reference distance. The group also addressed the naming convention, in light of the new data being generated for both widefield (WF) and spinning disk confocal (SDC) systems.
48th meeting, 17h of June 2025
Meeting date
17/06/2025 @ 5:00 PM (CET/CEST)
Meeting summary
LacJ presented a report from the last SC meeting. AzeM informed the group that a new OB representative is needed. The group discussed the recent modifications to the protocol made by DauA and agreed on the next steps to finalize it: DauA and AzeM will collaborate on developing the discussion section. It was also decided to begin acquiring new datasets using widefield (WF) and spinning disk confocal (SDC) systems. A new batch of slides containing 1 µm TetraSpeck beads will be sent to those interested in acquiring images. The group will take a summer break in July and August, with the next meeting scheduled for September 16th.
46th meeting, 15th of April 2025
Meeting date
15/04/2025 @ 5:00 PM (CET/CEST)
Meeting summary
WG04 members began the meeting by discussing feedback from the annual meeting. The author list on protocols.io was also addressed, and it was agreed that all co-authors should enter their full institutional address in the affiliation section under the “Organization” sub-tab.
The group also discussed the upload of WG04 data into OMERO and reviewed the adopted naming conventions.
Regarding next steps, members agreed to move forward with improving the first version of the WG04 protocol. The immediate goal is to adapt the protocol for use on confocal spinning disk and widefield microscopy systems.
44th meeting, 18th of February 2025
Meeting date
18/02/2025 @ 5:00 PM (CET/CEST)
Meeting summary
In the latest WG04 meeting, members reviewed the feedback received from a co-chair of another WG on the first version of the protocol. Final adjustments were discussed and agreed upon to refine the document before publication. Additionally, the group addressed authorship matters, ensuring proper acknowledgment of contributions and clarifying the necessary updates to affiliations on protocols.io.
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
12th meeting, 21st of February 2022
Meeting date
21/02/2022 @ 5:00 PM (CET/CEST)
Meeting summary
In this meeting we discussed:
- Revision of the WG7 main webpage on QUAREP.org
- Review progress done with WG2 to revise the Camera section of 4DN-BINA-OME-(QUAREP) Microscopy Metadata model in collaboration with Camera manufacturers and members of the Camera community.
- Review progress of SubGroup 2 (Metadata Education) and SubGroup 3 (Metadata Storage Specifications).
- Reminder: the novel SubGroup 4 (Model Revision) was formed but it did not convene yet because they are waiting for the end of the first phase of Camera community conversations. Please join us in this important work.
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.