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
41st meeting, 13th of May 2024
Meeting date
13/05/2024 @ 5:00 PM (CET/CEST)
Meeting summary
During the organisational and news part, the respective participants reported from the general assembly meeting which took place online on April 16th 2024. Subsequently, the steering committee (SC) was formed and held its inauguration meeting, which our SC members reported from as well. The main topic of our 41st meeting was to discuss and finalise our WG2 workshop on camera topics at ELMI2024. The workshop scheduled was presented, discussed, and approved. A new development was the joining of WG13 in our workshop withe the topic of avoidance of illumination overhead. In addition, we talked about the next steps to finalise and publish our protocols. A meeting with Emma Ganley from protools.io was planned for the next day. We will report from this meeting in the June meeting. As an additional topic, Gert-Jan introduced a possible new standardised light source which could be cheap and easy to built.
40th meeting, 8th of April 2024
Meeting date
08/04/2024 @ 5:00 PM (CET/CEST)
Meeting summary
After the organisational and news part, we started the meeting with the election of our SC representative, Britta Schroth-Diez, by acclamation.
The main topic of our 40th meeting was to discuss our potential contribution to the ELMI2024 community space. As a prerequisite we talked about the needed steps to finalise and ideally publish our protocols until ELMI2024 in June or July. One option is to have a preliminary version and check it during ELMI. We have to ensure to keep the protocols simple with trouble-shooting tips and tricks, also including instructive videos. We will work in smaller groups on the protocols until the May meeting.
For our WG2 contribution to the ELMI2024 community space, we are going to do a similar scenario as done last year. Focus will be on ongoing work to automate the workflow. We will also mention our work on the camera glossary. The presenters will meet to prepare a workshop schedule to be shown and discussed during our May meeting.
39th meeting, 11th of March 2024
Meeting date
11/05/2024 @ 5:00 PM (CET/CEST)
Meeting summary
Part of the meeting was planned to be the announcement of the results for our election of our WG2 co-chairs and representatives to the new governing bodies of QUAREP-LiMi (ERB, OB, SC). Unfortunately, we had some difficulties with the online voting platform. Therefore, we decided to do the elections via acclamation during the meeting. Results of the elections are: Co-chairs (for the next 2 years term): Gert-Jan Bakker, Valeria Berno, David McFadden, and Britta Schroth-Diez. ERB representative: David Grunwald, OB representative: Gerhard Holst. SC representative election will take place in our April meeting.
The main topic of our 39th meeting was to discuss our potential contribution to the ELMI2024 community space. We agreed to do a similar workshop as we did last year, with particularly focusing on automation of the workflow and presentation of our protocols. To be able to do so, we need to finalise and ideally publish our protocols until ELMI2024 in June. To be able to do so, we formed two smaller groups to go over the protocols again until the April meeting. In addition to our protocols efforts, we aim to also finalise the joined WG2-7camera glossary project and keep working on our first paper.
38th meeting, 12th of February 2024
Meeting date
12/02/2024 @ 5:00 PM (CET/CEST)
Meeting summary
The main topic of the meeting was the presentation of the by-law initiative by David Grundwald. You can find the current versions of the by-law documents and the slide deck of the by-law presentation in our 38th meeting folder. The by-laws and their approval will also be the main topic of our QUAREP-LiMi general assembly meeting on April 16th 2024.
In addition to this important topic we also discussed our potential contribution to the community space during ELMI 2024. We agreed to discuss this in more detail during our March meeting.
Gert-Jan gave a literature pitch about a very interesting Mulit-photon microsocpy QC paper published recently in bioRxiv. His presentation can be found in our 38th meeting folder as well,
In addition, it was reported that the first version of the camera model and glossary is finished. It will be revisited and discussed by the camera model revision stakeholder group before it will be presented as a suggestion for model change to the whole QUAREP-LiMi consortium. The meeting finished with a short summary and reminder about the work to be done towards our paper.
37th meeting, 11th of December 2023
Meeting date
11/12/2023 @ 5:00 PM (CET/CEST)
Meeting summary
In short, the main topic of this meeting was to discuss a potential collaboration with the MetrologyJ_QC group. For that, Orestis and Julien joined us as guests.
We found that both our efforts are complementary and thus can nicely be combined. The MetrologyJ_QC analysis tool focusses on calculating camera read noise, DSNU (dark signal non-uniformity), and hot and cold pixels. Our WG2 analysis tool focusses on calculating the photon-conversion factor. In addition, we as WG2 aim to combine our analysis with an easy to use (automated) acquisition protocol.
Generally, QUAREP-LiMi needs to develop a nice overarching framework for running all our quality control scripts automatically together easily in one tool. Someone needs to take the lead for this endeavour. There is already great groundwork being done, thanks to Kees, for WG1 and also for WG2.
In addition to this main topic there was the report from the last WG9 and WG7 meetings as well as a short review of the next steps to be done toward our paper.
36th meeting, 13th of November 2023
Meeting date
13/11/2023 @ 5:00 PM (CET/CEST)
Meeting summary
After a short session of QUAREP-LiMi news and updates on our other running projects, we mainly focussed on our planned paper which should accompany the publishing of our protocols. We discussed main aspects, determined topics which need to be addressed and members who our responsible for working on the topics. To be able to have time to do so, we decide to skip the meeting in January 2024.
Working Group 3
Working Group 4
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.
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!
Working Group 5
Working Group 6
Working Group 7
29th meeting, 17th of June 2024
Meeting date
17/06/2024 @ 5:00 PM (CET/CEST)
Meeting summary
Julio presented an extension to OMERO for tracking metrology data. During the discussion next steps were discussed which included attending WGs 3, 4, and 5 and presenting the work in order to align the metadata schema. There were also extended discussions about recent events, e.g., at OME2024 and ELMI2024.
Working Group 8
Working Group 9
Working Group 10
27th meeting, 11th of April 2023
Meeting date
11/04/2023 @ 4:00 PM (CET/CEST)
Meeting summary
For this meeting, we will need to take a decision about SBR parameter and all over parameter we decided not to consider.
+ 10 min per sub group to discuss briefly the progresses that have been made.
+ preparation of the Annual meeting
Working Group 11
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.