WG 2 – Detection system performance

At the beginning of our meeting, we shared information from the SC meeting: a big NSF grant was approved and process for finding a better suited name for our model was agreed.

Next, we discussed the proposed names for the model to replace NBO-Q and agreed that WG2 endorses the suggestions by WG7: LiMi Model. Our camera part of the model is still in the process of being finished, one more meeting round needs to be organised. Specifically, the definitions and describing texts for pixels (as picture elements) and dexels (as detector elements) need to be finalised. We discussed the suggested definitions and text drafts. In the last part of the meeting, the paper subgroup reported about their progress. The content of the work in progress will be shared on the QUAREP-LiMi cloud, in a folder privat to the paper subgroup.

We started the meeting with discussing our summer meeting scenario. Due to a public holiday and ELMI 2025, we decided to shift our June meeting to June 23rd. In addition, we decided to skip the meetings in July and August to have time for finishing the camera model and glossary, work on the paper, and have time for vacation. We decided to start again with the regular meeting schedule on September 8th.

This summer meeting organisation was followed by a report from the May steering committee meeting. One great news for WG2 was that the SC endorsed the terminology “dexel” for the detector element versus “pixel” as picture element. Next, we briefly discussed the current status of our ELMI workshop preparation.

This was followed by a report from the QUAREP-LiMi OMERO subgroup meeting. A naming convention was introduced by that subgroup, which everybody needs to follow. We discussed how to implement our spreadsheet terms and how to best automate the upload to OMERO. The WG2 co-chairs will look over tags and naming structure for WG2.

This discussion was followed by an update from the NBO-Q camera model and glossary group. The stakeholder group finished working on the hardware part and will now continue with the settings. The plan is to be finished by the end of this summer.

The WG2 paper working group reported from their first meeting where they summarised paper-related content from our past meeting minutes.

We finalised the meeting with summarising the next steps: finalise the NBO-Q camera model and glossary, work on our paper and collect data for it, support WG7 in their work to calibration metadata, and generalise the automation of our WG2 protocols collection to have it eventually working on all microscopy platforms.

After the usual short organisational matters and news section, we started right away with an overview over the work done on our protocols collection since the last meeting.

There have been done updates to the figures and figure legends, and all links have been checked and updated. All authors gave their consent to their respective authorship, author order, and listed contributions. Author contributions and funding are listed in each protocol via two respective pdfs in the acknowledgment section. In addition, we looked at an example protocol run including how to add comments, to see the difference between viewing a protocol versus running it.

Subsequently, we went through the collection and all protocols to have a last check of the respective content. Several small but significant changes were made. An exhaustive list of this changes can be found in our meeting minutes. We agreed to collect and save all images and figures used for the protocols on the QUAREP-LiMi cloud. A folder will be set up for this in the WG2 work done folder.

At 6:20 PM we did publish our protocols collection. You can find the titles and DOI links below.

After this great achievement we had the pleasure of welcoming our new member Nicolas Stifani from Montreal.

For finalising our other current major project, the NBO-Q camera model and glossary, there are four meetings scheduled in January. There will be a detailed report about this project in the February meeting. In addition, in the next meeting we will take time to discuss the next steps and goals for our future WG2 work.

2. Sample Preparation – An Easy-to-Prepare Sample Slide

DOI: dx.doi.org/10.17504/protocols.io.x54v92b91l3e/v1

3. Data Generation – Systems with an Area Detector

DOI: dx.doi.org/10.17504/protocols.io.bp2l62eorgqe/v1

4. Data Generation – Systems with a Point Detector

DOI: dx.doi.org/10.17504/protocols.io.j8nlk8176l5r/v1

We started the meeting with a short discussion about our meeting day, time, and length of the meeting. In the end we decided to keep the current scenario of meeting each second Monday of a month for 90mins from 5:00 – 6:30 PM CET. This discussion was followed by a short report from the last two QUAREP-LiMi SC meetings. The main message for us was that the SC approved of our request to publish our protocols collection. This approval included the conditions that we solve all open comments and clarify author contributions following the CreDiT taxonomy. It was suggested to us to add a document to each protocol with the respective author’s contribution list. The reminder of the meeting we used to go through the comments at the collection, the protocol 1. introduction, had a quick look at the protocol 2. – Sample Preparation, and started going through the comments of protocol 3. Data Generation – Systems with Area Detector. Since there were quite a few very helpful last minute comments, we did not manage to finish going through the protocols. We are still aiming to finish and publish before the holiday season. Therefore, we decided to meet again this week Thursday, December 12th, from 4-5PM CET in the WG2 zoom room. Everybody is welcome to join.

At the end of the meeting we briefly talked about the current status of the NBO-Q camera model and glossary project. We finished the series of meetings revisiting the hardware part of the model after the first change updates. The latest changes are being added to the model. The debriefing group is working on preparing the settings part of the model. Another stakeholder meeting series will be organised for January 2025.

We closed the meeting by having a quick look at the list of To Do’s for next year.