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
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.
Working Group 3
Working Group 4
40th meeting, 15th of October 2024
Meeting date
15/10/2024 @ 5:00 PM (CET/CEST)
Meeting summary
LacJ shared the key points discussed during the SC meeting on 2024/10/01 and presented the work on the data model to the WG members. The group focused on discussing the organization and content of the protocol, and deadlines were set to ensure its finalization. Our next WG meeting will be on November 19th.
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.
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
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
Working Group 9
Working Group 10
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!
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).
Working Group 11
33rd 10th of October 2024
Meeting date
10/10/2024 @ 11:00 AM (CET/CEST)
Meeting summary
Paula shares that bare-minimum checklist is moving forward. It took on new momentum at BINA meeting. SC endorsed content at Oct. SC meeting. Caterina and Judith are aligning with NBO-Q schema.
Some topics have been discussed.
Decission Tree for chosing reporting structure. Paula collected input from last meeting
MicCheck tree updates. is there a way to align MicCheck with quarep work?
Can users actually answer questions at the level of MicCheck?