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
Working Group 6
Working Group 7
40th meeting, 9th of March 2026
Meeting date
09/03/2026 @ 5:00 PM (CET/CEST)
Meeting summary
Topics:
1) WG7 Participation in the ELMI Meeting
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It was agreed that WG7 will submit an abstract for a community workshop at ELMI, focused on the LiMi-Model.
Also, it was decided that WG7 will support WG2 on a workshop or poster about the LiMi-Model_Camera revision process and outcome.
2) Discussion on the LiMi-Model website and LiMi-Model Viewer
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Participants were requested to provide feedback on the following three topics (please find details in the minutes document):
1) The LiMi-Model Viewer functionality
2) The LiMi-Model Viewer legend
3) The BP document
3) Content of the ELMI LiMi-Model Workshop
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This workshop will serve as the first major outreach effort for the LiMi-Model, covering its purpose, governance structure, and the ways in which community members can engage and contribute.
To provide a broader context, the workshop will open with an introductory presentation situating the LiMi-Model within the wider landscape of community metadata initiatives, including REMBI, imaging modality ontologies (such as FBbi and EDAM), and Next Generation Metadata schema definition languages. This aims to bring greater clarity to the range of ongoing efforts in the field.
The workshop will cover the following topics:
– Presentation of the LiMi-Model website
– Presentation of the model visualisation (prepared by Antony)
– Overview of model governance and contribution pathways
39th meeting, 19th of January 2026
Meeting date
19/01/2026 @ 5:00 AM (CET/CEST)
Meeting summary
WG7 met to kick off 2026 with introductions, including a few new faces, and a round where everyone shared their wishes for the year ahead. The group caught up on ongoing work around light microscopy metadata, including LiMi-Model, REMBI alignment, and links to efforts beyond bioimaging. We discussed updates on repositories, community coordination, and the fact that several new full-time positions have now been funded to work specifically on metadata extensibility. Looking ahead, the group plans a future presentation on the Czech national strategy for metadata, and agreed on a handful of practical next steps to keep the different efforts better aligned.
38th meeting, 17th of November 2025
Meeting date
03/11/2025 @ 5:00 PM (CET/CEST)
Meeting summary
The following decisions were made regarding the revision of the QC/Performance Extension of the NBO-Q (aka LiMi Model)
DECISION 1: “QC/QC Run” shall be fused with “QC/QA assay”
DECISION 2: DateTime and ProtocolUsed fields will be added to both Sample and Experiment
NEXT STEP: CONSENSUS: invite people from QUAREP WG12 and BINA Informatics WG to present about the current state of the art. Ask them to provide a representative who will be available to present at our next meeting.
37th meeting, 15th of September 2025
Meeting date
15/09/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Discussion about the new name for the NBO-Q model: WG7 will present the three finalist names to the SC and present the pros and cons of each of the three names. At the same time, a vote was held to determine the preferred name of WG7.
2) Update on the status of the NBO-Q webpage: Anthony presented progress towards an interactive viewer of the NBO-Q to be used for the website.
3) REMBI-DCAT-AP presentation: Marek Cebecauer presented work performed by the Czech Core Metadata Model (CCMM) initiative to build a DCAT-based REMBI schema.
4) Announcement of the successful funding of the Imaging-Persistent Hardware Descriptor (PHD) project to assign persistent identifiers to individual microscopes and their hardware descriptors.
36h meeting, 16th of June 2025
Meeting date
16/06/2025 @ 5:00 PM (CET/CEST)
Meeting summary
We had an extended conversation about the naming of the NBO-Q model, eliminating some of the previous suggestions and adding a few new which will be sent out to WG7 again for further voting. We also looked at the status of the website update and reported on discussions from ELMI.
35th meeting, 5th of May 2025
Meeting date
05/05/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Worked on aligning attributes from the “MetricDataset”, “MetricsOutput” and “KeyMeasurements” classes of microscopemetrics-schema
with NBO-Q
NEXT STEPS:
Discuss with Julio ML about the mapping and questions that were put forth during this meeting
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.