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
42nd meeting, 10th of June 2024
Meeting date
10/06/2024 @ 5:00 PM (CET/CEST)
Meeting summary
After agreeing to take a summer break and skip our August meeting, we discussed the QUAREP-LiMi workshop contributions to ELMI. One workshop was held by WG5 and the other one jointly by WG2 and WG13 members. Both workshops were well received. Several questions were raised during our joined WG2-WG13 workshop and also during discussions afterwards. These need to be addressed when finalising our protocols. Discussing the steps and the timeline towards publishing our protocols was the next point on our meeting agenda. Participants reported from the meeting with Emma Ganley from protocols.io. Based on that we decided to best publish our protocols in form of a protocols collection. Smaller subgroups will work on the protocols until the July meeting. If need be, we will use the August meeting date for a dedicated protocols hackathon. We aim to present the finished collection to the QUAREP-LiMi steering committee in early fall.
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.
Working Group 3
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.
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.
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
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.
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
30th meeting, 12th of March 2024
Meeting date
12/03/2024 @ 4:00 PM (CET/CEST)
Meeting summary
This meeting will be dedicated to a quick review of the RID parameter, a global discussion about the new parameter AS told us about and importantly, the ByLaws document with the need of volunteer candidates for the various positions (SC, EBR, OB).
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
