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
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
8th meeting, 6th of May 2021
Meeting summary
WG 5 have principally been testing beads for PSF measurements, using different formats (polystyrene, DNA origami, nanodots, printed patterns). We have identified an optimal size range for confocal and widefield imaging, and a re still testing the ease of use, functionality and robustness of several of these formats. We have begun a draft methodology which we propose to publish for Confocal PSF measurement using beads before developing the method further for other modalities, as well as investigating alternative methods, such as mirrors for axial resolution tests.
Working Group 6
Working Group 7
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.
16th meeting, 18th of July 2022
Meeting date
18/07/2022 @ 5:00 PM (CET/CEST)
Meeting summary
Despite considerable progress (publications, collaborations with other working groups, feedback from manufacturers, further development of metadata collection tools, educational material, outreach, etc.), participation has been waning.
To address this issue, we discussed the following topics:
1) What can we do to improve motivation and participation?
2) What should be our goals for the upcoming year?
The discussion was very animated and participated. Several constructive suggestions were made. In summary:
1) Having subgroups allows to achieve tasks, but it can be very confusing. It is important to improve the organization of the work and communication to members on what needs to be done and what is done:
– agreed upon, small, and achievable tasks
– clear schedule (always advertised on the QUAREP calendar)
– report back consistency on goals and progress
2) It is important to shift focus from Microscopy Metadata to Experimental/Sample Metadata capture. Would it make sense for WG7 to be involved in developing standards around these topics?
3) It is important to develop guidelines but for work to be successful and productive, WG7 has to be involved with developers to produce tools that implement the guidelines and bring them to life for imaging scientists.
Next steps:
– The August meeting is canceled. See you back in September
– In September, all Subgroups will have a meeting to organize next year’s schedule (regular or not?) goals and activities.
– Co-Chairs will meet to decide whether a survey to collect feedback on future goals is needed for all WG7 members (even those that do not participate in sub-groups).