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Working Group 1

25th meeting, 2nd of February 2023

Meeting date

02/02/2023 @ 5:00 PM (CET)

Meeting summary

Summary of last meeting by Nathalie.

Feed-back from subgroups:
  • Glossary subgroup only worked on camera part, not the illumination part.
  • CAD files for power meter sensor holders have been loaded on the GitHub.
Recently, a new holder for Thorlabs slides in a shape that fits into a multi-well plates holders has been made in Freiburg. Works only for inverted microscopes. Automation: Arne Fallish is working on a program analysing the data recorded with Thorlabs power meter, eventually feed data back to Zeiss Software. We should try to involve big companies more in the automation and encourage them to develop macros. Nathalie shows the new layout of the protocol, made by her and Laurent, to remove step cases and use collapsible notes: Britta discussed the issue with people from Protocol.io and they may investigate it, but right now step-cases are branching out and one cannot come back into the main common/root protocol. Roland indicates that the meeting with Emma has been recorded. One should be able to get in from our QUAREP Cloud. Britta suggests that appendices should be moved in an ad hoc section, if Protocol.io creates one, or we should have a dedicated box in the other sections, since the appendices are not steps and do not belong to the protocol. Another option is to create a pdf and add it to the description section. We will aslo ask protocols.io for an abbreviation box under the description tab. We will ask all WG1 participants, e.g., co-authors of version 1, to read the new protocol before we publish. If we do not here from them, it means that we can keep their names. Britta suggests asking feed-back from all QUAREP members to make sure we do not overlap and contradict part of their work. We agreed. Nathalie will investigate if in protocol.io we could have the endorsement separate from authorship. We screened the videos made by Laurent on power meter usage. We will add the logo of QUAREP on all slides. Also add the corresponding steps from the protocol. We will also consider a submission to PLOS ONE protocols. We finally made improvements to the protocol, based on WG1 members comments.

Meeting documentation

24th meeting, 7th of December 2022

Meeting date

07/12/2022 @ 5:00 PM (CET)

Meeting documentation

23rd meeting, 2nd of November 2022

Meeting date

02/11/2022 @ 5:00 PM (CET)

Meeting summary

We recapitulated the last changes in steps 1 to 4 of the protocol, and reviewed the new Question 19 about broad-band illumination sources in Appendix 1. We then further adapted steps 5 to 8 to cover new illumination/microscopy modalities.

Meeting documentation

Subgroup Automation, 4th meeting, 9th of September 2022

Meeting date

09/09/2022 @ 5:00 PM (CET)

Meeting documentation

22nd meeting, 7th of September 2022

Meeting date

07/09/2022 @ 5:00 PM (CET)

Meeting summary

We briefly discussed progress made by our sub- groups and completed the review of the appendix 1b generated by Manfred on power meter settings for other light source. We all agreed to merge it to appendix 1. We also reviewed and discussed comments and suggestions posted in protocols.io. We now have updated step 1 through 4 of the protocols to include other illumination sources and wide-field systems.

Meeting documentation

21st meeting, 3rd of August 2022

Meeting date

08/03/2022 @ 5:00 PM (CET)

Meeting summary

We welcomed two new members of WG1: Katarzyna Cialowicz and Kurt Weiss.

News from the subgroups: Glossary: a first document with a mission statement is to be found in the new folder WG1-MetaDataModel. This is in coordination with WG7, as it has been also done in WG2. The subgroup will try to have as many companies on board as possible. Automation: no meeting since last time. Power meter: see below paragraph on “Appendix 1b”.

Appendix 1b: Measuring Broadband Light Sources. We rephrased the introductory sentence and the first paragraph on Lasers. We then discussed the relevant operations for a broadband illumination. We identified at least three important parameters that may influence the absolute power measurement: the spectrum of the light source, the specifications of the excitation filter set and of the dichroic, and the responsivity of the power meter sensor. However, to make the measurement easier and robust, we agreed on a convention: the wavelength to be set on the power meter should be in the middle of the bandpass of the excitation filter. Note that if the measurement is done within the linear range of the responsivity curve of the power meter, using the center of the bandpass is a way of averaging responsivity values. The specific spectrum of the light source within the excitation bandpass should not have any significant influence on a biological experiment, and is not getting further consideration here.

Meeting documentation

Working Group 2

31st meeting, 12th of June 2023

Meeting date

12/06/2023 @ 5:00 PM (CET)

Meeting documentation

30th meeting, 8th of May 2023

Meeting date

08/05/2023 @ 5:00 PM (CET)

Meeting documentation

29th meeting, 17th of April 2023

Meeting date

17/04/2023 @ 5:00 PM (CET)

Meeting documentation

28th meeting, 13th of March 2023

Meeting date

13/03/2023 @ 5:00 PM (CET)

Meeting summary

  1. First we discussed some general QUAREP-LiMi news:
    • QUAREP-LiMi is now a community partner of image.sc, we potentially need to contribute to the moderating in the future
    • there is a community room at ELMI for QUAREP and other imaging communities to do 6 workshops, WG2 member contribution is welcome
    • the French MetrologyJ-QC group is very interested in a collaboration with us in WG2, we will invite them to a future WG2 meeting
    • WG12 paper is in the review process of Nature methods
  2. Second we collected ideas on which topics to discuss in the breakout room. It was agreed to especially include open questions and problems: challenge how to measure sensitivity; our strategy of community roll-out; current problems we are facing: UUIDs; data handling, storage, and retrieval. We also collected some potential survey questions. A small team was formed to prepare the breakout room, the short introduction video and questions for a possible survey; all of which will be presented during our next WG2 meeting.
  3. Third followed the reports from the small group measurement teams: for sample preparation, we now have the text for the marker-pen sample on protocols.io (please check it out). A text is planned for the Chromaslide ramp. MathiasH went to the EMVA1288 certification course. He will report in our next meeting.
We closed the meeting by agreeing on the next steps.

Meeting documentation

27th meeting, 13th of February 2023

Meeting date

13/02/2023 @ 5:00 PM (CET)

Meeting summary

After first talking about organisational news, we discussed the changes in date and plans for our upcoming QUAREP-LimI general assembly meeting. It is going to be held online on April 26th 2023 3-6PM. We decided that we want to participate with our own breakout room and formed a small preparation team which will also think about potential questions for a survey. A short video presentation needs to be prepared as well. Next the small measurement teams reported their results. Team CET focussed on test samples and found the marker pen as bright enough, easy to prepare and use. Team CET2 focused on the protocol and its usability via protocols.io. There is still a lot of optimization to do (changing the order of the steps, optimizing the run behavior of the protocol). This discussion was followed by the report from our training session with Emma Ganley from the protocols.io team. At the end of the meeting we summarized the main next steps: simplify our protocols and the protocols structure, and updated our detection system behavior measurement excel sheet. The APE measurement reporting session is planned for our June meeting.

Meeting documentation

26th meeting, 9th of January 2023

Meeting date

09/01/2023 @ 5:00 PM (CET)

Meeting summary

We used the opportunity of this being the first meeting in 2023 to look back at our achievements, but also challenges, last year. As a main challenge we identified the motivation and organisation for collecting data and analysing it. This is essential to test and optimise our protocols to be able to finalise and subsequently publish them. We therefore decided to form small groups of 3-4 people doing the measurements together. In addition, we discussed to have our aims and next steps smaller and more tight, focus on one aim only. This way we will steadily move forward to eventually reach our goal. Our protocols group gave a brief update on the development of our WG2 protocols in the protocols.io QUAREP-LiMi workspace and informed about the planned training session with Emma Ganley from the protocols.io team. At the end of the meeting we summarised the main next steps: do measurements in the small groups and contact the protocols.io support team about our needs.

Meeting documentation

Working Group 3

23rd meeting, 13th of June 2023

Meeting date

13/06/2023 @ 5:00 PM (CET)

Meeting documentation

22nd meeting, 11th of April 2023

Meeting date

11/04/2023 @ 5:00 PM (CET)

Meeting documentation

21st meeting, 14th of March 2023

Meeting date

14/03/2023 @ 5:00 PM (CET)

Meeting documentation

20th meeting, 9th of February 2023

Meeting date

09/02/2023 @ 5:00 PM (CET)

Meeting documentation

19th meeting, 12th of January 2023

Meeting date

12/01/2023 @ 5:00 PM (CET)

Meeting documentation

18th meeting, 7th of December 2022

Meeting date

07/12/2022 @ 5:00 PM (CET)

Meeting documentation

Working Group 4

28th meeting, 18th of July 2023

Meeting date

18/07/2023 @ 5:00 PM (CET)

Meeting documentation

27th meeting, 20th of June 2023

Meeting date

20/06/2023 @ 5:00 PM (CET)

Meeting documentation

26th meeting, 16th of May 2023

Meeting date

16/05/2023 @ 5:00 PM (CET)

Meeting documentation

25th meeting, 18th of April 2023

Meeting date

18/04/2023 @ 5:00 PM (CET)

Meeting documentation

24th meeting, 21st of March 2023

Meeting date

21/03/2023 @ 5:00 PM (CET)

Meeting documentation

23rd meeting, 21st of February 2023

Meeting date

21/02/2023 @ 5:00 PM (CET)

Meeting documentation

Working Group 5

29th meeting, 15th of June 2023

Meeting date

15/06/2023 @ 3:30 PM (CET)

Meeting documentation

28th meeting, 11th of May 2023

Meeting date

11/05/2023 @ 3:30 PM (CET)

Meeting documentation

27th meeting, 13th of April 2023

Meeting date

13/04/2023 @ 3:30 PM (CET)

Meeting documentation

26th meeting, 9th of March 2023

Meeting date

09/03/2023 @ 3:30 PM (CET)

Meeting documentation

25th meeting, 9th of February 2023

Meeting date

09/02/2023 @ 4:00 PM (CET)

Meeting documentation

24th meeting, 8th of December 2022

Meeting date

08/12/2022 @ 3:30 PM (CET)

Meeting documentation

Working Group 6

23rd meeting, 10th of May 2023

Meeting date

10/05/2023 @ 4:00 PM (CET)

Meeting documentation

22nd meeting, 12th of April 2023

Meeting date

12/04/2023 @ 4:00 PM (CET)

Meeting documentation

21st meeting, 8ht of March 2023

Meeting date

08/03/2023 @ 4:00 PM (CET)

Meeting documentation

20th meeting, 8th of February 2023

Meeting date

08/02/2023 @ 4:00 PM (CET)

Meeting documentation

19th meeting, 11th of January 2023

Meeting date

11/01/2023 @ 4:00 PM (CET)

Meeting documentation

18th meeting, 14th of December 2022

Meeting date

14/12/2022 @ 4:00 PM (CET)

Meeting documentation

Working Group 7

24th meeting, 26th of June 2023

Meeting date

26/06/2023 @ 5:00 PM (CET)

Meeting documentation

23rd meeting, 7th of June 2023

Meeting date

07/06/2023 @ 3:00 PM (CET)

Meeting documentation

22nd meeting, 15th of May 2023

Meeting date

15/05/2023 @ 5:00 PM (CET)

Meeting documentation

Subgroup Capture Tools, 7th meeting, 19th of April 2023

Meeting date

19/04/2023 @ 5:00 PM (CET)

Meeting documentation

Subgroup Model, 7th meeting, 3rd of April 2023

Meeting date

03/04/2023 @ 5:00 PM (CET)

Meeting documentation

21st meeting, 20th of March 2023

Meeting date

20/03/2023 @ 5:00 PM (CET)

Meeting documentation

Working Group 8

4th meeting, 10 of November 2020

Meeting documentation

3rd meeting, 29th of October 2020

Meeting documentation

2nd meeting, 8th of October 2020

Meeting documentation

1st meeting, 16h of September 2020

Meeting documentation

Working Group 9

25th meeting, 27th of June 2023

Meeting date

27/06/2023 @ 4:00 PM (CET)

Meeting documentation

24th meeting, 2nd of May 2023

Meeting date

02/05/2023 @ 4:00 PM (CET)

Meeting documentation

23rd meeting, 4th of April 2023

Meeting date

04/04/2023 @ 4:00 PM (CET)

Meeting documentation

22nd meeting, 7th of March 2023

Meeting date

07/03/2023 @ 4:00 PM (CET)

Meeting documentation

21st meeting, 7th of February 2023

Meeting date

07/02/2023 @ 4:00 PM (CET)

Meeting documentation

20th meeting, 6th of December 2022

Meeting date

06/12/2022 @ 4:00 PM (CET)

Meeting documentation

Working Group 10

24th meeting, 13th of December 2022

Meeting date

13/12/2022 @ 4:00 PM (CET)

Meeting summary

After last meeting tasks distribution for our 5 parameter sub-groups, it is time for a progress report.

Meeting documentation

23rd meeting, 8th of November 2022

Meeting date

08/11/2022 @ 8:59 PM (CET)

Meeting summary

For this new meeting, we are going to have a close look to a parameter-free resolution estimation based on decorrelation analysis thanks to Guillaume Gay (France BioImaging).

Meeting documentation

22nd meeting, 11th of October 2022

Meeting date

11/10/2022 @ 4:00 PM (CET)

Meeting summary

The WG10 is back after summer break. A new organization will be proposed and a distribution of the tasks to be accomplished will be made. A V2 document will be presented too. We hope to see many of you on this occasion!

Meeting documentation

21st meeting, 12th of July 2022

Meeting date

12/07/2022 @ 4:00 PM (CET)

Meeting documentation

20th meeting, 14th of June 2022

Meeting date

14/06/2022 @ 4:00 PM (CET)

Meeting documentation

19th meeting, 10th of May 2022

Meeting date

10/05/2022 @ 4:00 PM (CET)

Meeting documentation

Working Group 11

20th meeting, February 23rd 2023

Meeting date

23/02/2023 @ 10:51 AM (CET)

Meeting documentation

18th meeting, 9th of February 2023

Meeting summary

In order to get the finalized draft, we agreed on having the next meeting in two weeks. We will meet on Thursday Feb 9th at 11 am EST, 5pm CEST. We will start our discussion from the “Detectors” section. The only homework assigned to you is to read the current checklist document and start thinking about how you feel about the metadata items to be ready to have another great discussion. We will work on the checklist, but we will update the mind map too.

Meeting documentation

17th meeting, 26th January 2023

Meeting date

26/01/2023 @ 10:29 AM (CET)

Meeting summary

We are looking forward to continuing our work on publishing standards with you. As suggested, we are dedicating 1.5 h to our recurring meeting, which happens on the 4th Thursday of the month, at 11 am Boston time, 5 pm Berlin time. Thank you!  

Meeting documentation

16th meeting, 22nd December 2022

Meeting date

22/01/2023 @ 5:00 PM (CET)

Meeting documentation

15th meeting, 30th of November 2022

Meeting date

30/11/2022 @ 5:00 PM (CET)

Meeting documentation

14th meeting, 27th of October 2022

Meeting date

27/10/2022 @ 5:00 PM (CET)

Meeting documentation