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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

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.

Meeting documentation

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.

Meeting documentation

28th meeting, 13th of March 2023

Meeting date

13/03/2023 @ 5:00 PM (CET/CEST)

Meeting summary

  1. 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
  2. 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.
  3. 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.
We closed the meeting by agreeing on the next steps.

Meeting documentation

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.

Meeting documentation

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.

Meeting documentation

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.

Meeting documentation

Working Group 3

30th meeting, 13th of February 2024

Meeting date

13/02/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

29th meeting, 9th of January 2024

Meeting date

09/01/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

28th meeting, 12th of December 2023

Meeting date

12/12/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

27th meeting, 14th of November 2023

Meeting date

14/11/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

26th meeting, 17th of October 2023

Meeting date

17/10/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

25th meeting, 5th of September 2023

Meeting date

05/09/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

Working Group 4

37th meeting, 21st of May 2024

Meeting date

21/05/2024 @ 5:00 PM (CET/CEST)

Meeting summary

WG4 acknowledges the acceptance of the QUAREP by-laws. Judith Lacoste serves as the WG4 Steering Committee (SC) representative, Ileana Micu as the Editorial Review Board (ERB) representative, and Christian Kukat as the Ombuds Board (OB) representative. Also, Maria Azevedo is now co-chair with Aurélien Dauphin. An overarching publication involving WG03, WG04, WG05, and a microscope manufacturer was discussed, and suggestions for WG04 representatives to participate were put forward. An update on the naming convention was provided, and the group discussed what should be included for WG04 datasets. Importantly, WG04 will not meet in June; however, an email containing updates on the naming convention and instructions to test OMERO will be sent. The next WG04 meeting is scheduled for July 16th.

Meeting documentation

36th meeting, 24th of April 2024

Meeting date

24/04/2024 @ 5:00 PM (CET/CEST)

Meeting summary

A microscope manufacturer is using the QUAREP protocols to provide time-0 measurments before shipping units to its customers. The manufacturer‘s team presented on what seems to be a code implementation issue for the calculation of the reference surface used to calculate the co-registration performance with the tool MetroloJ QC. With the supporting references, they show that the way code is currently written, the 3D reference surface is rendered as a peanut shape instead of an ovoid elongated sphere. As a result of this, the XY and Z co-registration accuracy is not correctly assessed. The authors of MetroloJ_QC will be contacted to present them these findings and ask for feedbacks.

Meeting documentation

35th meeting, 19th of March 2024

Meeting date

19/03/2024 @ 5:00 PM (CET/CEST)

Meeting summary

WG04 pursues the analyses of 1um beads datasets for color co-registration, comparing different software. There was a discussion regarding measurements of signal to background ratio on aging bead preparations. The group discussed about how detectors settings and metadata can have an impact on the co-registration analysis results. Please note the next WG04 monthly meeting date. It was moved because of QUAREP annual meeting. Lastly, many thanks to the members who agreed to become co-chairs and representatives of WG-04: Maria Azevedo, Aurélien Dauphin, Christian Kukat, Judith Lacoste and Ileana Micu.

Meeting documentation

34th meeting, 20th of February 2024

Meeting date

20/02/2024 @ 5:00 PM (CET/CEST)

Meeting summary

Today the proposed QUAREP by-laws were presented. WG04 is grateful to those who worked with David Grunwald for the preparation of this impressive document. The by-laws will be submitted for approval during the QUAREP annual meeting next April. In the mean time, WG04 is asking its members to come forward for the following positions in our workgroup: WG04 co-chairs, a WG04 steering committee representative, a WG04 editorial review board representative and a WG04 ombuds board representative. In addition, QUAREP will need to elect 13 persons on the steering committee and 3 persons on the ombuds board. Our organisation just reached 600 members, for sure there will be new people joining on the above committees to make QUAREP better. Please let us know of your interest in the above positions. A big thanks in advance!

Meeting documentation

33rd meeting, 16th of January 2024

Meeting date

16/01/2024 @ 5:00 PM (CET/CEST)

Meeting documentation

32nd meeting, 19th of December 2023

Meeting date

19/12/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

Working Group 5

42nd meeting, 19th of September 2024

Meeting date

14/09/2024 @ 3:30 PM (CET/CEST)

Meeting documentation

41st meeting, 11th of July 2024

Meeting date

11/07/2024 @ 3:30 PM (CET/CEST)

Meeting documentation

40th meeting, 13th of June 2024

Meeting date

13/06/2024 @ 3:30 PM (CET/CEST)

Meeting summary

We discussed the ELMI workshop, including how it went and what we could improve. We also covered the process of OMERO uploads and linking them to Airtable for tracking results, as well as the filenaming nomenclature.

Meeting documentation

39th meeting, 24th of May 2024

Meeting date

24/05/2024 @ 3:30 PM (CET/CEST)

Meeting documentation

38th meeting, 4th of April 2024

Meeting date

04/04/2024 @ 3:30 PM (CET/CEST)

Meeting documentation

37th meeting, 14th of March 2024

Meeting date

13/03/2024 @ 3:30 PM (CET/CEST)

Meeting documentation

Working Group 6

5th meeting, 14th of July 2021

Meeting documentation

4th meeting, 12th of May 2021

Meeting documentation

3rd meeting, 13th of April 2021

Meeting documentation

2nd meeting, 10th of March 2021

Meeting documentation

1st meeting, 10th of February 2021

Meeting documentation

Working Group 7

25th meeting, 18th of September 2023

Meeting date

18/09/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

24th meeting, 26th of June 2023

Meeting date

26/06/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

23rd meeting, 7th of June 2023

Meeting date

07/06/2023 @ 3:00 PM (CET/CEST)

Meeting documentation

22nd meeting, 15th of May 2023

Meeting date

15/05/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

Subgroup Capture Tools, 7th meeting, 19th of April 2023

Meeting date

19/04/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

21st meeting, 20th of March 2023

Meeting date

20/03/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

Working Group 8

Working Group 9

16th meeting, 7th of July 2022

Meeting date

07/07/2022 @ 4:00 PM (CET/CEST)

Meeting documentation

15th meeting, 5th of May 2022

Meeting date

05/05/2022 @ 4:00 PM (CET/CEST)

Meeting documentation

14th meeting, 5th of April 2022

Meeting date

05/04/2022 @ 4:00 PM (CET/CEST)

Meeting documentation

13th meeting, 3rd of March 2022

Meeting date

03/03/2022 @ 4:00 PM (CET/CEST)

Meeting documentation

12th meeting, 1st of February 2022

Meeting documentation

11th meeting, 7th of December 2021

Meeting documentation

Working Group 10

23rd meeting, 8th of November 2022

Meeting date

08/11/2022 @ 8:59 PM (CET/CEST)

Meeting summary

For this new meeting, we are going to have a close look to a parameter-free resolution estimation based on decorrelation analysis thanks to Guillaume Gay (France BioImaging).

Meeting documentation

22nd meeting, 11th of October 2022

Meeting date

11/10/2022 @ 4:00 PM (CET/CEST)

Meeting summary

The WG10 is back after summer break. A new organization will be proposed and a distribution of the tasks to be accomplished will be made. A V2 document will be presented too. We hope to see many of you on this occasion!

Meeting documentation

21st meeting, 12th of July 2022

Meeting date

12/07/2022 @ 4:00 PM (CET/CEST)

Meeting documentation

20th meeting, 14th of June 2022

Meeting date

14/06/2022 @ 4:00 PM (CET/CEST)

Meeting documentation

19th meeting, 10th of May 2022

Meeting date

10/05/2022 @ 4:00 PM (CET/CEST)

Meeting documentation

18th meeting, 22nd of February 2022

Meeting date

22/02/2022 @ 4:30 PM (CET/CEST)

Meeting documentation

Working Group 11

26th meeting, 7th of December 2023

Meeting date

07/12/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

25th meeting, 26th of October 2023

Meeting date

26/10/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

24th meeting, 28th of September 2023

Meeting date

28/09/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

23rd meeting, 25th of May 2023

Meeting date

25/05/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

22nd meeting, 27th of April 2023

Meeting date

27/04/2023 @ 5:00 PM (CET/CEST)

Meeting documentation

21st meeting, March 23rd 2023

Meeting date

24/03/2023 @ 12:00 AM (CET/CEST)

Meeting summary

1-We will review the Bare Minimal Requirements Checklist for “Methods” journals. You can all review it here: https://nextcloud.quarep.org/index.php/s/544SCiDkKHns9rj
2-We are also switching gears and will continue with the WG11 mission, which as you all know will include more comprehensive requirements. Below, please find the link to the document we will be working with today.

Meeting documentation