Working Group 1
10th meeting, 2nd of June 2021
Meeting summary
We reviewed comments in the main document, discussing comments and suggestions and adding tips on safety, environmental conditions, and type of laser used. We also discussed the potential damages a laser can cause to an objective, the difference in laser power measurements obtained from different laser power meter brands/sensors and the effect of temperature on your measurements. The subgroups “Automation” and “Powermeter” reported briefly their progress.
9th meeting, 5th of May 2021
Meeting summary
We reviewed comments in the main document, discussed discrepancy between measurements made with different power meter models on the same microscope and same laser, commented different graphs to display all measurements made by the group in their respective labs so far, to help define what a “stable” behavior is. We decided to set up a Zotero shared library for reference articles. The automation sub-group presented the project of a GitHub repository for scripts.
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
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
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).
