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.
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.
Working Group 3
Working Group 4
49th meeting, 16th of September 2025
Meeting date
16/09/2025 @ 5:00 PM (CET/CEST)
Meeting summary
LacJ updated the group on the latest news from QUAREP-LiMi. The group then discussed the results and the discussion section of the protocol, and it was agreed to include the data obtained using MetroloJ_QC, where the experimental distance is normalized to the reference distance. The group also addressed the naming convention, in light of the new data being generated for both widefield (WF) and spinning disk confocal (SDC) systems.
48th meeting, 17h of June 2025
Meeting date
17/06/2025 @ 5:00 PM (CET/CEST)
Meeting summary
LacJ presented a report from the last SC meeting. AzeM informed the group that a new OB representative is needed. The group discussed the recent modifications to the protocol made by DauA and agreed on the next steps to finalize it: DauA and AzeM will collaborate on developing the discussion section. It was also decided to begin acquiring new datasets using widefield (WF) and spinning disk confocal (SDC) systems. A new batch of slides containing 1 µm TetraSpeck beads will be sent to those interested in acquiring images. The group will take a summer break in July and August, with the next meeting scheduled for September 16th.
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.
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.
Working Group 5
Working Group 6
Working Group 7
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.
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
18th meeting, 9th of February 2023
Meeting summary
In order to get the finalized draft, we agreed on having the next meeting in two weeks. We will meet on Thursday Feb 9th at 11 am EST, 5pm CEST.
We will start our discussion from the “Detectors” section. The only homework assigned to you is to read the current checklist document and start thinking about how you feel about the metadata items to be ready to have another great discussion.
We will work on the checklist, but we will update the mind map too.
17th meeting, 26th January 2023
Meeting date
26/01/2023 @ 10:29 AM (CET/CEST)
Meeting summary
We are looking forward to continuing our work on publishing standards with you. As suggested, we are dedicating 1.5 h to our recurring meeting, which happens on the 4th Thursday of the month, at 11 am Boston time, 5 pm Berlin time. Thank you!