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
12th meeting, 11th of October 2021
Meeting summary
One of the main topics of our meeting was to prepare for the joint meeting with WG7 on establishing standardized vocabulary for describing cameras. The idea for this meeting is to bring together camera manufacturers, microscope companies, and users to agree upon the vocabulary.
In addition, we have to test and finalize both, our measurement and the analysis protocols, by generating more data for determination of the photo-conversion factor (PCF) and background. For that we agreed to use a de-focused Chroma slide edge as main test sample for now.
Last, we discussed how to get more members actively involved and keep the active ones motivated.
11th meeting, 13th of September 2021
Meeting summary
This was the first meeting after the summer break. Therefore we mainly did a status update of the current standing of WG2 and our 4 subgroups (area detector, point detector, analysis, test samples). Mainly, first data sets were collected using the first versions of our measurement protocols. Also, we have a first version of a stand-alone analysis program for retrieving of the photon-conversion factor and dark noise contribution. We discussed the documentation and organization of the data and meta data collected, how to improve it, and how to interact with the MetaDataApp.
Working Group 3
Working Group 4
6th meeting, 18th of May 2021
Meeting summary
We have generated a detailed protocol and are currently testing the following parameters: 1) how does bead size affect the coregistration accuracy. We test 200nm, 1µm, and 5µm beads at the moment. 2) are the suggested settings from the iso manual neccessary, or can we generate a more convenient protocol. We test the impact of pixel size and z-step size (16nm/40nm, and 70/200nm).
From first measurements, we have seen that a variation from speciment preparation can be rather high. Thus, one of us (Aurelien) is creating the samples for the rest of WG4.
Working Group 5
Working Group 6
Working Group 7
Subgroup Model 2nd Meeting, 5th of October 2022
Meeting date
05/10/2022 @ 4:00 PM (CET/CEST)
Meeting summary
–Caterina and Mathias are having a series of twice-a-week in-person meetings at UMass Med to produce a revised version of the NBO-Q model Excel Spreadsheet that incorporates all proposals for change that emerged from the series of meetings with Camera Manufacturers (referred to as JOINT CAMERA FEEDBACK GROUP)
The product should be done in 1 month.
–This revised spreadsheet will be used as a starting point for our work as well as to solicit a final round of feedback from the JOINT CAMERA FEEDBACK GROUP.
–We will use LinkML as the framework to represent the metadata model. LinkML core format is YAML but a SPREADSHEET can be used as the core representation from which other representations can be generated.
DECISIONS:
NEXT MEETING ON 11/7/2022 AT 11 am ET and then every 1st Monday after that
LinkML will be tested to support the production of different interlinked representations of the model
17th meeting, 19th of September 2022
Meeting date
19/09/2022 @ 5:00 PM (CET/CEST)
Meeting summary
The work of QUAREP-WG7 is done within WG7-Subgroups that have clear goals listed on the WG7 homepage (https://quarep.org/working-groups/wg-7-metadata/).
The general meeting serves as a space for reporting back on the progress that has been achieved within the Subgroups, connecting the dots, strategic planning, and general discussions.
This organization allows WG7 to carry out several parallel tasks that span from image metadata model specifications, the development of metadata collection tools, the improvement of the metadata storage formats, and the development of educational and training material to onboard biomedical researchers.
DECISIONS:
- The general organization of WG7 is sound, and it will be maintained.
- To leave more time for Subgroup work and reduce time waste, it was decided that we will reduce the frequency of WG7 general meeting while making Subgroup meetings regular and consistent.
- Specifically, the general meeting will be held on the third Monday once every 2 months —> NEXT GENERAL MEETING will be on 11/21/2022 (17:00 CEST / 11:00 EST)
- The same slot will be utilized as needed by the subgroups. For example, the next WG7-Subgroup 2 meeting will take place on the 17th of October (17:00 CEST / 11:00 EST).
- At the same time, it is essential to improve communication and progress management to make sure people have a clear idea of what is happening, and how they can contribute.
- To facilitate the division of labor and communication, we will create granular task lists in Excel and link the list from the WG7 homepage (https://nextcloud.quarep.org/index.php/s/DgJBQnjg3jSMgx8). The list will be bae on the tasks emerging from Sub-Group meetings, will provide precise instructions, and include clear due dates (e.g. Subgroup 1: TASK = provide feedback on Micro-Meta App Confocal canvases; DUE=10/17/2022)
Subgroup Model, 1st meeting, 19th of September 2022
Meeting date
19/09/2022 @ 4:00 PM (CET/CEST)
Meeting summary
This was the kick-off meeting for Subgroup 4 of WG7 on Metadata. The purpose of this working group is to revise the published 4DN-BINA-OME Microscopy Metadata model on the basis of feedback from commercial manufacturers and the imaging community.
As a starting point, we are going to revise the Camera model.
During this meeting we described the current status of the work conducted by the WG2-WG7-Camera Manufacturers series of feedback meetings to revise the NBO-Q Camera metadata specifications:
– GitHub —> https://github.com/WU-BIMAC/NBOMicroscopyMetadataSpecs/tree/master/Model/in%20progress/v02-10/Components/Detector
– GoogleDrive —> https://drive.google.com/drive/folders/1uCjLqRj9jS1pBXmFlk7sOUIrJCVeCrZS?usp=sharing
After that, we started discussing the specifics of the requested changes.
In particular, we discussed how to implement the concept of CAMERA OPERATIONAL MODE.
For more details, see the video recordings.