Working Group 1
15th meeting, 2rd of February 2022
Meeting summary
The automation sub-group led by Miso and Nasser presented the product of their hard work now located on GitHub. We all agreed that a link to this GitHub site will be accessible from the final and published version of our protocol in protocol.io. We also discussed interesting results collected by Orestis on the potential effects of temperature on laser stability. We think these should be used as a case study for our future troubleshooting section. Finally, we briefly discussed authorship (see WG9 guidelines) and the adoption of common sites and platforms by all WG of QUAREP including protocol.io, image.sc forum, youtube channel and GitHub repos. These will be the responsibility of WG9. We have created a list of future topics we will take on starting next month at our 16th WG1 meeting to be held on Wednesday March 2nd, 17:00-18:30 CET).
14th Meeting, 1st of December 2021
Meeting summary
We discussed privacy consideration for the data uploaded to the AirTable WG1 database and will discuss further with WG9 and AirTable the different options to limit visibility and access. We also finalized the main document, discussed the linearity protocol and adding more representative data. The protocol has been transferred to Protocol.io in a private account, it will be further updated and made accessible to all QUAREP members early next year. We also assigned the different appendices to different subgroups to work on a very first, publishable version of the power meter settings, automation measurements, impact of environmental factors, and troubleshooting sections.
13th Meeting, 3rd of November 2021
Meeting summary
We had 20 participants today and welcomed 3 new members. We presented Airtable, a new web-based platform for shared database. All previously collected data and new plots can be found on this Dashboard. Use the following Form to enter new data. You will need to sign in and create an account before getting access. We also reviewed very briefly some editing done by Laurent and Nathalie on the main document (formatting and reorganization) and a new draft version of the protocol uploaded on Protocol.io. Finally, we went over some example data of laser warming up presented by Laszlo. We all agreed that it should be included in our protocol.
12th Meeting, 6th of October 2021
Meeting summary
We reviewed the new introduction section, providing context, purpose and objectives for the laser power stability protocol.
We also discussed laser safety, alternative protocols and the results section.
For the results, the majority highly recommended to not present at once all the results we gathered (we don’t believe we have a representative sample yet), but preferably to provide typical examples of data, show how it should be analyzed, presented and communicated. We also proposed to include a template.
We discussed laser warm-up and proposed to include an appendix of example data for different systems.
Finally, we also reviewed briefly our appendices.
11th Meeting, 1st of September 2021
Meeting summary
We spent the meeting reviewing the edits and comments everyone made in the first two pages of the main document. Amongst other things, we discussed adding more specificity to the goal of this protocol in the introduction, proposed to emphasize Laser Safety remarks with bold text, references and symbols, to add a CAD file of Roland’s holder, and write system specific instructions to the appendix section. A Zotero group library has been created and link sent to all (please communicate with Nathalie if you need help including a reference).
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
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
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
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)