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
10th meeting, 19th of October 2021
Meeting summary
We are currently generating data in several locations and with several different confocal microscopes of the WG4 members. We defined three workflows to analyze the data with the aim to specify contributions of the analysis workflow on the results. We decided to use the suggestions (Meta App) from WG7 (metadata) to save all our metadata. Matadata will be extremely important to discuss our results, thus we established a set of metadata important for WG4 and collect them in a table for future analysis.
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
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.
Subgroup Model, 3rd meeting, 7th of November 2022
Meeting date
07/11/2022 @ 4:00 PM (CET/CEST)
Meeting summary
- Report back from Mathias and Caterina revision of the Camera Metadata Model based on the feedback from the JOINT CAMERA FEEDBACK GROUP Caterina and Mathias have completed the revision of the DETECTION SYSTEM 2022-10-07_NBO-Q_DETECTOR_v3-00-0_DRAFT_V01 spreadsheet (https://docs.google.com/spreadsheets/d/1KQgAClf4lp90sZ0egUez1h2HYwhvC5VFbaBn1mqvgqE/edit?usp=sharing) Caterina and Mathias have worked at testing LinkML as a framework that we could use to represent the metadata model and would allow the automatic generation of different representations starting from a unique source of truth. · Specifically the advantage of LinkML is that it can use a spreadsheet as the source of truth · The spreadsheet has to be following the schemasheet format (https://linkml.io/schemasheets/) o https://docs.google.com/spreadsheets/d/1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ/edit#gid=55566104 · Mathias and Caterina are testing the schemasheet format to see if it can be used as a source of truth
- Decide on more frequent schedule for follow up meetings · Mathias and Caterina will communicate when the schemasheet version of NBO-Q v3.00_DRAFT is ready to be discussed and presented · David, Mathias, Roland, and Britta will review the 2022-10-07_NBO-Q_DETECTION SYSTEM_v3-00-0_DRAFT_V01 spreadsheet (https://docs.google.com/spreadsheets/d/1KQgAClf4lp90sZ0egUez1h2HYwhvC5VFbaBn1mqvgqE/edit?usp=sharing) so that we can then present it to the CAMERA FEEDBACK GROUP to finalize the request for changes and produce a DRAFT v02 that can be used as a source of truth for implementation
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