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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:

  1. sanctions Working Groups to form teams that focus on specific technical or outreach topics;

  2. maintains, disseminates, and teaches best practices, protocols, and software tools; and

  3. 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 Phototoxicitywere 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

52nd meeting, 12th of May 2025

Meeting date

12/05/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

51st meeting, 14th of April 2025

Meeting date

14/04/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

50th meeting, 10th of March 2025

Meeting date

10/03/2025 @ 5:00 PM (CET/CEST)

Meeting summary

Agenda points

  1. Organizational matters and News
  2. Annual QUAREP-LiMi meeting
  3. ELMI 2025 workshop contribution
  4. Update on NBO-Q camera model & glossary
  5. Next steps

Meeting documentation

49th meeting, 10th of February 2025

Meeting date

10/02/2025 @ 5:00 PM (CET/CEST)

Meeting summary

This was our first meeting since the publication of our WG2 Protocols collection. Therefore, our main focus was to discuss the next steps for our work. 
We agreed on a key concern: how to collect data now that the protocol is available, and how we can assist users in automating the data collection process for use with the analysis tool. We agreed to use OMERO as our main tool. However, this will require significant work. We need to have an easy way to upload data to the OMERO server. Secondly, we need to determine the metadata necessary to support the main detector parameters that can be analysed using our published protocol tools.
Secondly, we got an update on the progress of the Camera Glossary and Model work. The hardware part is almost done. This will be followed by working on the settings part.
Finally, we decided to use the exciting possibility to present our Protocols collection by offering one or two workshops in the community room during the ELMI meeting in June 2025 in Heidelberg.

Meeting documentation

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

DOI: dx.doi.org/10.17504/protocols.io.eq2lyw5mevx9/v1

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

DOI: dx.doi.org/10.17504/protocols.io.rm7vzjew2lx1/v1

Meeting documentation

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.

Meeting documentation

Working Group 3

40th meeting, 13th of March 2025

Meeting date

13/03/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

39th meeting, 13th of February 2025

Meeting date

13/02/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

38th meeting, 9th of January 2025

Meeting date

09/01/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

37th meeting, 5th of December 2024

Meeting date

05/12/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

36th meeting, 14th of November 2024

Meeting date

14/11/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

35th meeting, 10th of October 2024

Meeting date

10/10/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

Working Group 4

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.

Meeting documentation

45th meeting, 18th of March 2025

Meeting date

13/03/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

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.

Meeting documentation

43rd meeting, 21st of January 2025

Meeting date

21/01/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

42nd meeting, 17th of December 2024

Meeting date

17/12/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

41st meeting, 19th of November

Meeting date

19/11/2024 @ 5:00 PM (CET/CEST)

Meeting summary

LacJ shared the key points discussed during the SC meeting on 2024/11/12. The remainder of the meeting was dedicated to discussing the outline and content of the protocol.

Meeting documentation

Working Group 5

49th meeting, 15th of May 2025

Meeting date

15/05/2025 @ 3:30 PM (CET/CEST)

Meeting documentation

48th meeting, 14th of April 2025

Meeting date

14/04/2025 @ 3:30 PM (CET/CEST)

Meeting summary

The protocol V2 was discussed and it was voted to pass the next version of the protocol to the SC. For the upcoming ELMI workshop, plans were initiated to host a one-hour session, considering point source and line patterns, and coordinating tasks among participants. An update on the paper shared insights on confocal SBR and r² values, noting differences due to noise factors. Discussions included data analysis techniques and the challenges of data variance over time. The meeting concluded with a call for organizing data in OMERO and an update on a new ISO norm for metadata, inviting community participation. The next meeting is postponed by a week to accommodate a French national holiday.

Meeting documentation

47th meeting, 13th of March 2025

Meeting date

13/03/2025 @ 3:30 PM (CET/CEST)

Meeting documentation

46th meeting, 13th of February 2025

Meeting date

13/02/2025 @ 3:30 PM (CET/CEST)

Meeting documentation

45th meeting, 9th of January 2025

Meeting date

09/01/2025 @ 3:30 PM (CET/CEST)

Meeting documentation

44th meeting, 14th of November 2024

Meeting date

14/11/2024 @ 3:30 PM (CET/CEST)

Meeting documentation

Working Group 6

40th meeting, 12th of March 2025

Meeting date

12/03/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

39th meeting, 5th of February 2025

Meeting date

05/02/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

38th meeting, 11th of December 2024

Meeting date

11/12/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

37th meeting, 13th of November 2024

Meeting date

13/11/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

36th meeting, 8th of October 2024

Meeting documentation

35th meeting, 14th of August 2024

Meeting date

14/08/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

Working Group 7

35th meeting, 5th of May 2025

Meeting date

05/05/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

34rd meeting, 23rd of April 2025

Meeting date

23/04/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 18th meeting, 7th of April 2025

Meeting date

07/04/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

Subgroup Model, 17th meeting, 3rd of March 2023

Meeting date

03/03/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

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.

Meeting documentation

32nd meeting, 16th of December 2024

Meeting date

16/12/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

Working Group 8

15th meeting, 28th of May 2025

Meeting date

28/05/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

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!).

Meeting documentation

13th meeting, 26th of March 2025

Meeting date

26/03/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

12th meeting, 26th of February 2025

Meeting date

26/02/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

11th meeting, 22nd of January 2025

Meeting date

22/01/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

10th meeting, 27th of November 2024

Meeting date

27/11/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

Working Group 9

34th meeting, 7th of May 2024

Meeting documentation

33rd meeting, 9th of April 2024

Meeting date

09/04/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

32nd meeting, 12th of March 2024

Meeting date

12/03/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

31st meeting, 6th of February 2024

Meeting date

06/02/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

30th meeting, 8th of January 2024

Meeting date

09/01/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

29th meeting, 5th of December 2023

Meeting date

05/12/2023 @ 4:00 PM (CET/CEST)

Meeting documentation

Working Group 10

37th meeting, 11th of March 2025

Meeting date

11/03/2025 @ 4:00 PM (CET/CEST)

Meeting summary

Today’s meeting is dedicated to a presentation and task division on the #NoFilter paper.

Meeting documentation

36th meeting, 11th of February 2025

Meeting date

11/02/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

35th meeting, 21st of January 2025

Meeting date

21/01/2025 @ 4:00 PM (CET/CEST)

Meeting documentation

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!  

Meeting documentation

33rd meeting, 12th of November 2024

Meeting date

12/11/2024 @ 3:00 PM (CET/CEST)

Meeting documentation

32nd meeting, 9th of July 2024

Meeting date

09/07/2024 @ 4:00 PM (CET/CEST)

Meeting documentation

Working Group 11

39th meeting, 24th of April 2025

Meeting date

24/04/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

38th meeting, 27th of March 2025

Meeting date

27/03/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

37th meeting, 27th of February 2025

Meeting date

27/02/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

36th meeting, 23rd of January 2025

Meeting date

23/01/2025 @ 11:00 AM (CET/CEST)

Meeting summary

We are going to have a discussion about the design of the “Minimal Checklist” for journals.

Meeting documentation

35th 05th of December 2024

Meeting date

05/12/2024 @ 11:00 AM (CET/CEST)

Meeting summary

We are going to have a final discussion on the “Minimal Checklist” for journals. WG7 has been working very hard to align the checklist with the Metadata model.

Meeting documentation

34th 24th of October 2024

Meeting date

24/10/2024 @ 10:00 AM (CET/CEST)

Meeting documentation