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
18th meeting, 11th of April 2022
Meeting date
11/04/2022 @ 5:00 PM (CET/CEST)
Meeting summary
At the beginning of our 18th meeting, we talked about a few organisational matters and shared general QUAREP-LiMi news: the next general assembly will take place May 25th 2022, 4-6PM CEST.
This was followed by reports from the the last two WG2 & WG7 camera glossary meetings. The main topic for both meetings was what defines a colour camera. It was reported that that joined discussion group also needs input from WG2 about what we require the model to deliver. The ensuing discussion pointed out: commonly used glossary and definitions, to be used in methods sections, for spec sheets, TIER level needed with minimal specs required and additional specs available upon request.
The APE Quantiflash test samples will be shipped to their first testes soon. The transfer of our data collection to Airtable is under way. More infos to both topics will come in the next meeting.
Last but not least, we discussed the next steps towards finalising the first part of our protocols and moving them to protocol.io following the example and experience of WG1. Until the next meeting, each subgroup will look at their respective protocol draft, go over the text and identify open questions. We agreed to finalise the structure with a general introduction and branching or similar feature for the AD and PD protocols. The aim is to have a teaser ready for ELMI, publish the protocol in autumn.
To be able to do so, we need to have more people test the protocols, measurement and analysis.
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.
Working Group 5
48th meeting, 14th of April 2025
Meeting date
14/04/2025 @ 3:30 PM (CET/CEST)
Meeting summary
The protocol V2 was discussed and it was voted to pass the next version of the protocol to the SC.
For the upcoming ELMI workshop, plans were initiated to host a one-hour session, considering point source and line patterns, and coordinating tasks among participants.
An update on the paper shared insights on confocal SBR and r² values, noting differences due to noise factors. Discussions included data analysis techniques and the challenges of data variance over time. The meeting concluded with a call for organizing data in OMERO and an update on a new ISO norm for metadata, inviting community participation. The next meeting is postponed by a week to accommodate a French national holiday.
Working Group 6
Working Group 7
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!
18th meeting, 21st of November 2022
Meeting date
21/11/2022 @ 5:00 PM (CET/CEST)
Meeting summary
Caterina reported that all the to-do items from last meeting have been completed. Created a granular task list based on what are tasks identified in each of the Sub-Groups and a link to spreadsheet was added to WG7 mainpage. In addition a proposal was tabled to announce QUAREP-WG7 meetings on Image.sc and it was agreed at the meeting. Ken reported the OME-Meeting on Metadata. Josh’s talk can be found here https://www.openmicroscopy.org/events/ome-community-meeting-2022/ · Great material for advocating about the need of a NG Metadata framework, although no clear definition of storage location. There were much discussion of Nature Methods and Nature Cell Biology request to QUAREP-LiMi to develop a light microscopy checklist for Nature Portfolio. Caterina reported back that we had initial meeting with Rita and Melina to discuss Nature requirements and initial meeting with WG7, 9, 11 and 12 chairs to dicuss next steps. We aim to provide the checklist by Christmas to Nature Methods. Nature is not going to release the data, but something that they will like to work and discuss with their editors.
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
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?