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
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.
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.
28th meeting, 13th of March 2023
Meeting date
13/03/2023 @ 5:00 PM (CET/CEST)
Meeting summary
- 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
- 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.
- 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.
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.
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.
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.
Working Group 3
Working Group 4
Working Group 5
Working Group 6
6th meeting, 8th of September
Meeting summary
Meeting continued to focus on details of the measuring protocol proposed. Discussion on test targets, beads vs slide etching etc. A stronger call to action to add to the protocol, make suggestions is needed. An excel worksheet should be instituted to list up all major changes to the protocol, who proposed, suggested changes, supporting documentation etc. This excel document should be used to review / accept the changes and produce a modified clean copy to circulate to WG chairs for comment.
Working Group 7
Subgroup Model, 6th meeting, 6th of March 2023
Meeting date
06/03/2023 @ 5:00 PM (CET/CEST)
Meeting summary
The main topic of the meeting was the discussion of the NBO-Q Microscopy Metadata Map. The Map aims to facilitate the distribution of responsibilities among WGs regarding the documentation of Microscope Hardware, Acquisition Settings, and Quality Control procedures.
Caterina presented the schema she prepared and received feedback.
As a result of the feedback, the map was updated.
The current version of the map can be found here: https://nextcloud.quarep.org/index.php/s/E3AKjNMbWgXDN3B
20th meeting, 20th of February 2023
Meeting date
20/02/2023 @ 5:00 PM (CET/CEST)
Meeting summary
During the meeting we discussed the following items:
1) Next meeting will be held on March 20th 2023 and then we will continue every two months on the 3rd Monday.
2) Reminders will be sent 1 month, 1 week, 1 day, and 1 hour before each meeting.
3) The work of the WG will continue to concentrate on revising the 4DN-BINA-OME Microscopy Metadata Model and, as much as possible, will attempt to maintain compatibility with REMBI as a high-level set of recommendations.
4) WG7 works to collect the requirements of all WGs and create a consensus that incorporates the metadata requirements of all other WGs. As such WG7 works as an underlying platform on which all other WGs can build. It is important that we do a better job to explain to the QUAREP’s community that our work should be conceived as spanning across multiple WGs.
5) We need a general map of all components of the model, how they relate to each other, and which is the responsibility of which WGs
6) WG7 would like to have time during the annual meeting to discuss with everyone on this!
Subgroup Model, 5th meeting, 6th of February 2023
Meeting date
06/02/2023 @ 5:00 PM (CET/CEST)
Meeting summary
Discussion concerned primarily on review of current model revision activities and how to best handle the proposal/review/acceptance/implementation process when faced with the need to revise the NBO-Q model. Consensus:
At the moment we are volunteer-driven and changes will have to be done on the basis of individuals taking the lead, driving a revision, putting together a revision and then submitting to the rest of the group for review, acceptance and implementation
In this context, when a team of individuals is putting lots of work in making changes and they request feedback it would be great if people would take into account the amount of work that was done and be respectful
Going forward we will need a formal method to propose/review/accept/implement changes to the model as the current model is not going to work for developers [a rough estimate would indicate that10000 hours of development are going to be needed for each model request for-change)
RE: Camera model revision to increase efficiency concentrate on producing minimal description for each field and in a second round work on a more extensive glossary