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
48th meeting, 13th of January 2025
Meeting date
13/01/2025 @ 5:00 PM (CET/CEST)
Meeting summary
After the usual short organisational matters and news section, we started right away with an overview over the work done on our protocols collection since the last meeting.
There have been done updates to the figures and figure legends, and all links have been checked and updated. All authors gave their consent to their respective authorship, author order, and listed contributions. Author contributions and funding are listed in each protocol via two respective pdfs in the acknowledgment section. In addition, we looked at an example protocol run including how to add comments, to see the difference between viewing a protocol versus running it.
Subsequently, we went through the collection and all protocols to have a last check of the respective content. Several small but significant changes were made. An exhaustive list of this changes can be found in our meeting minutes. We agreed to collect and save all images and figures used for the protocols on the QUAREP-LiMi cloud. A folder will be set up for this in the WG2 work done folder.
At 6:20 PM we did publish our protocols collection. You can find the titles and DOI links below.
After this great achievement we had the pleasure of welcoming our new member Nicolas Stifani from Montreal.
For finalising our other current major project, the NBO-Q camera model and glossary, there are four meetings scheduled in January. There will be a detailed report about this project in the February meeting. In addition, in the next meeting we will take time to discuss the next steps and goals for our future WG2 work.
Collection:
Characterization of the Photon Conversion Factor, Noise, and Dynamic Range of Light Microscope Detection Systems
Separate protocols:
1. Introduction – Background and Aims
2. Sample Preparation – An Easy-to-Prepare Sample Slide
DOI: dx.doi.org/10.17504/protocols.io.x54v92b91l3e/v1
3. Data Generation – Systems with an Area Detector
DOI: dx.doi.org/10.17504/protocols.io.bp2l62eorgqe/v1
4. Data Generation – Systems with a Point Detector
DOI: dx.doi.org/10.17504/protocols.io.j8nlk8176l5r/v1
5. Analysis – Characterization of the Photon Conversion Factor, Noise, and Dynamic Range
47th meeting, 9th of December 2024
Meeting date
09/12/2024 @ 5:00 PM (CET/CEST)
Meeting summary
We started the meeting with a short discussion about our meeting day, time, and length of the meeting. In the end we decided to keep the current scenario of meeting each second Monday of a month for 90mins from 5:00 – 6:30 PM CET. This discussion was followed by a short report from the last two QUAREP-LiMi SC meetings. The main message for us was that the SC approved of our request to publish our protocols collection. This approval included the conditions that we solve all open comments and clarify author contributions following the CreDiT taxonomy. It was suggested to us to add a document to each protocol with the respective author’s contribution list. The reminder of the meeting we used to go through the comments at the collection, the protocol 1. introduction, had a quick look at the protocol 2. – Sample Preparation, and started going through the comments of protocol 3. Data Generation – Systems with Area Detector. Since there were quite a few very helpful last minute comments, we did not manage to finish going through the protocols. We are still aiming to finish and publish before the holiday season. Therefore, we decided to meet again this week Thursday, December 12th, from 4-5PM CET in the WG2 zoom room. Everybody is welcome to join.
At the end of the meeting we briefly talked about the current status of the NBO-Q camera model and glossary project. We finished the series of meetings revisiting the hardware part of the model after the first change updates. The latest changes are being added to the model. The debriefing group is working on preparing the settings part of the model. Another stakeholder meeting series will be organised for January 2025.
We closed the meeting by having a quick look at the list of To Do’s for next year.
46th meeting, 11th of November 2024
Meeting date
11/11/2024 @ 5:00 PM (CET/CEST)
Meeting summary
After the usual short organisational matters and news section, we started our meeting with the presentation by David Grunwald about his soon to be published MetaMax manuscript. MetaMax is a tool hat can be used for detector calibration. The main request from David is to check if there is any input from our WG2 work that needs to be acknowledged. You can find the manuscript and a document for your comments in our 46th meetings folder.
Next Britta presented a request from WG1 to review version 3 of its protocol on measuring illumination power and stability. Version 3 now contains also measurement requirements for multi-photon systems. In addition, it has an improved table of contents and its text was modified for clarity and accuracy. Please give comments, feedback, and endorsement directly in protocols.io until end of November.
The NBO-Q camera model ad glossary is planned to be finished by the end of this year. To achieve this, three new stake holder meeting dates were announced (Nov 11th, Nov 22nd, Dec 4th). A lock-in meeting to prepare the settings part is planned on Dec 4th. Please watch out for the invitation emails.
The main part of our meeting was again dedicated towards finalising our WG2 protocols collection. We got several helpful and positive comments from WG2 members and also members from other WGs. The most urgent comment was for us to clarify our aim 1. We discussed this and agreed on a version. For the reminder of the meeting we split into two break out rooms to work on the collection, protocols 1 (introduction) and 5 (analysis) in one room and protocols 2 (sample prep) and 3 and 4 (data collection) in the other room. Since we did not manage to finish, we agreed to have extra meetings to work on the protocols (see meeting minutes for exact dates and time). Our aim is to present the final collection to the steering committee on December 3rd for approval to publish.
Addendum: Britta presented our protocols collection draft during the SC meeting on November 12th. We got the OK to present our collection for publication approval in the December 3rd meeting.
45th meeting, 14th of October 2024
Meeting date
14/10/2024 @ 5:00 PM (CET/CEST)
Meeting summary
We started the meeting with a brief report from the last steering committee meeting followed by a short report about the current status of the work at the NBO-Q camera model and glossary. The camera model work is progressing steadily. We aim to finish the hardware part first and then continue with the settings part. To prepare well for this, a small group will meet beginning of December. More stakeholder meetings will take place in October and November.
The main part of our meeting was spent working on our protocols collection. By now we reserved the DOIs for later publication and sent emails to the co-chairs of the other WGs to ask for feedback. We discussed to also present during upcoming meetings of other WGs if possible and appropriate. We aim to publish the collection until the end of 2024. For that we need to either present in the SC meeting in November or December.
Decision will be made in our November WG2 meeting. The reminder of the meeting we worked on our protocols collection going through the comments we already received there.
44th meeting, 9th of September 2024
Meeting date
09/09/2024 @ 5:00 PM (CET/CEST)
Meeting summary
After the summer break, the WG2 meeting was a good opportunity to redefine our deadlines for completing our protocol collection.
We discussed guidelines and disclaimers, the collection of new sample images, and formed small groups to finalize each protocol for sending out our collection for testing and comments to the whole QUAREP-LiMi community as soon as possible.
WG2, together with WG7, is also involved in finalizing the camera model and glossary part of the NBO-Q model schema. To conclude the revision process, we will hold three further meetings with the stake-holder group still this month.
The preparation of both, the protocol collection as well as the NBO-Q camera model and glossary, is very important for achieving our next goal, the publication of our first paper.
43rd meeting, 8th of July 2024
Meeting date
08/07/2024 @ 5:00 PM (CET/CEST)
Meeting summary
Since we had previously decided to skip our regular WG2 August meeting, we agreed to use August for finalising our protocols. On August 19th we will meet at our usual WG2 time (5:00 – 6:30PM CEST) for a protocols collection hackathon. This discussion was followed by short reports from the QUAREP-LiMi SC meeting, from the Dutch microscopy association, and about a new QC white paper by evident. During the subsequent agenda point we talked about the next steps towards finalising the NBO-Q camera model and glossary. First final revision meetings by the stakeholder groups were planned for July.
The main agenda point of our 43rd meeting was discussing the next steps towards finalising our protocols for publication. We agreed on the following timeline: until August 19th finalise separate protocols, put them into one collection during the hackathon on August 19th, get the protocols collection tested theoretically and practically and collect example measurements until October 14th. Implement comments and example measurements until November 11th (our WG2 meeting) and present the final protocols collection to the QUAREP-LiMi steering committee on November 12th. To finalise our separate protocols, we formed four small teams who will organise respective discussion meetings. For this version of the protocols collection we decided to keep separate protocols for point and area detectors, respectively. We plan to add protocols based on the French QC paper in the next version of our protocols collection.
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
33rd meeting, 17th of February 2025
Meeting date
17/02/2025 @ 5:00 PM (CET/CEST)
Meeting summary
The meeting covered updates on France BioImaging’s metadata efforts, including OMERO.quay beta testing, buffer server deployment, and authentication improvements. WG10 discussed defining “raw” images and their metadata requirements, emphasizing the need for clarity on file formats. The website report highlighted the need for better organization and visibility of resources, with a proposal to create a landing page and potentially rebrand NBO-Q. Discussions on synonyms and profiles addressed term mapping challenges and possible alias extensions. Additional topics included a McGill student project porting NBO-Q to LinkML and preparations for an ISO discussion at OME2025. The next meeting date requires rescheduling due to Easter.
31st meeting, 21st of October 2024
Meeting date
21/10/2024 @ 5:00 PM (CET/CEST)
Meeting summary
The following topics were discussed:
- Report back on work done by members of the WG to align the terminology used in the upcoming WG11 checklist with NBO-Q
- Mandate from the SC to WG7 to generate an NBO-Q landing page.
- The primary target audience for the NBO-Q landing page is QUAREP members.
- The NBO-Q landing page will start by simply delineating the data model and why it is essential to the QUAREP mission. Subsequently, more content, including examples and visualizations, will be added gradually. A group of volunteers were identified to work on moving this project forward. They will present their work during the next meeting.
- In all we do, it is essential to advance together and develop consensus with all members of QUAREP. To this aim, it is crucial to educate all members of QUAREP on what metadata is, how metadata can be represented in machine and human-readable manners, and why organizing metadata in a model is essential.
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
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.