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Working Group 1

26th meeting, 1st of March 2023

Meeting date

01/03/2023 @ 5:00 PM

Meeting summary

The subgroup for automation has developed a new script for Zeiss instrument that makes the old one obsolete. It will be uploaded on the website soon. Other participants also inform that more scripts for Leica and Visitron are being developed. We also all agreed on the fact that the GitHub is a living repository and will evolve with time, even when the protocols are done. We then reviewed the latest comments on the protocol and made small improvements to it. We decide to keep the stability formula as it is, even though it might be very sensitive to one outlier and does not reflect always what is wrong. However, we agree that to know there is an outlier or something is wrong is already very important, and one has to plot the stability curve anyhow, and can thereby immediate see why the stability value might be low. Nathalie explains the process for co-authorship and endorsement. We will ask WG chairs to read and say is they want to co-sign or endorse “works for me” through protocol.io. QUAREP general assembly: Laurent will prepare a presentation. Survey: we will align with Roland.

Meeting documentation

25th meeting, 2nd of February 2023

Meeting date

02/02/2023 @ 5:00 PM

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

Meeting documentation

23rd meeting, 2nd of November 2022

Meeting date

02/11/2022 @ 5:00 PM

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

Meeting documentation

22nd meeting, 7th of September 2022

Meeting date

07/09/2022 @ 5:00 PM

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

Working Group 2

28th meeting, 13th of March 2023

Meeting date

13/03/2023 @ 5:00 PM

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

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

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

25th meeting, 12th of December 2022

Meeting date

12/12/2022 @ 5:00 PM

Meeting summary

We started with a brief report from WG9&co-chairs last meeting, focusing mainly on the next general assembly meeting of QUAREP-LiMi. In this meeting, we then had a big discussion on Metadata. There is a specific need of finding a good way to collect, name and recover image files.Try to find an agreement on naming the file isn’t universally acceptable. Therefore, the idea is to find a way to recover the most important metadata on acquisition parameters and device settings in a unique format. Omero could be the answer and it requires a list of metadata. In the same direction is also the request from Nature protocol and other editors for publication.

Meeting documentation

24th meeting, 14th of November 2022

Meeting date

14/11/2022 @ 5:00 PM

Meeting summary

Thanks a lot to all of you who participated in the lively discussion about our “Detection system behaviour measurements” collection. We discussed several aspects of the table structure for our measurements and analysis data wich needs to be updated. One major discussion was again about the unique identifier. A solution needs to be found in general for Quarep. Until then we use an intermediate solution with unique identifiers in our excel sheet. Also need to ask the HTS community for their expertise. Furthermore, Kees reported from his last test runs with the APE quantiflash. His presentation can also be found here on our cloud folder. The other test places will report about their experiences and results in our meeting in February.

Meeting documentation

23rd meeting, 10th of October 2022

Meeting date

10/10/2022 @ 5:00 PM

Meeting summary

We did start our meeting welcoming a new member and refresh a few organisational matters. This was followed by the report from the WG9 & cochair meeting on Oct 6th: – More active members are needed for WG9. – Furthermore, an internal review process was discussed. Please revise and comment on the proposal for the “Internal Review Pipeline”. The joined group WG2and WG7 is working to consolidate the camera part of the model. The glossary still needs to be finished. A new organisation of model revision was discussed as well as potential next topics: light sources (maybe two parts: lasers, wide-field illumination), filters, objectives. We then focused the discussion on AirTable organisation and reporting of measurement and parameters from acquisition and analysis. As a result of the discussion we agreed to start from excel file in order to define the most important parameter before to transfer all of them in AirTable. Care should be taken in naming and saving the data in the correct way so that the analysis group can focus on the output parameters and their interpretation. Acquisition parameters and issue still need to be fixed and all comments should be added to the protocol draft in protocols.io once it is finalised there. (A QUAREP-LiMi-wide training on ptrotocols.io was planned for beginning of November.) Still work to do in: testing new samples (marker pen), acquire new images from chroma slide, collect and compare analysis measurements, finalise the transfer of our protocols after the training.

Meeting documentation

Working Group 3

21st meeting, 14th of March 2023

Meeting date

14/03/2023 @ 5:00 PM

Meeting documentation

20th meeting, 9th of February 2023

Meeting date

09/02/2023 @ 5:00 PM

Meeting documentation

19th meeting, 12th of January 2023

Meeting date

12/01/2023 @ 5:00 PM

Meeting documentation

18th meeting, 7th of December 2022

Meeting date

07/12/2022 @ 5:00 PM

Meeting documentation

17th meeting, 10th of November 2022

Meeting date

10/11/2022 @ 5:00 PM

Meeting documentation

16th meeting, 13th of October 2022

Meeting date

13/10/2022 @ 5:00 PM

Meeting documentation

Working Group 4

24th meeting, 21st of March 2023

Meeting date

21/03/2023 @ 5:00 PM

Meeting documentation

23rd meeting, 21st of February 2023

Meeting date

21/02/2023 @ 5:00 PM

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22nd meeting, 17th of January

Meeting date

17/01/2023 @ 5:00 PM

Meeting documentation

21st meeting, 15th of December 2022

Meeting date

15/12/2022 @ 4:00 PM

Meeting documentation

20th meeting, 16th of November

Meeting date

16/11/2022 @ 4:00 PM

Meeting documentation

19th meeting, 20th of September 2022

Meeting date

20/09/2022 @ 5:00 PM

Meeting summary

Discuss the transition of the protocol to protocols.io.  Members of WG4 are invited to put comments to keep developing the protocol for WG4 via protocols.io.  Discussion on data/metadata management and the use of a microscopy image database (e.g. OMERO) in the future to progress faster.  Discussion on data analysis strategies and sharing the results with AirTable and/or spreadsheets.

Meeting documentation

Working Group 5

26th meeting, 9th of March 2023

Meeting date

09/03/2023 @ 3:30 PM

Meeting documentation

25th meeting, 9th of February 2023

Meeting date

09/02/2023 @ 4:00 PM

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24th meeting, 8th of December 2022

Meeting date

08/12/2022 @ 3:30 PM

Meeting documentation

23rd meeting, 10th of November

Meeting date

10/11/2022 @ 3:30 PM

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22nd meeting, 13th of October

Meeting date

13/10/2022 @ 3:30 PM

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21st meeting, 15th of September 2022

Meeting date

15/09/2022 @ 3:30 PM

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Working Group 6

21st meeting, 8ht of March 2023

Meeting date

08/03/2023 @ 4:00 PM

Meeting documentation

20th meeting, 8th of February 2023

Meeting date

08/02/2023 @ 4:00 PM

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19th meeting, 11th of January 2023

Meeting date

11/01/2023 @ 4:00 PM

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18th meeting, 14th of December 2022

Meeting date

14/12/2022 @ 4:00 PM

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17th meeting, 16th of November 2022

Meeting date

16/11/2022 @ 4:00 PM

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16th meeting, 14th of September 2022

Meeting date

14/09/2022 @ 4:00 PM

Meeting documentation

Working Group 7

Subgroup Model, 6th meeting, 6th of March 2023

Meeting date

06/03/2023 @ 5:00 PM

Meeting summary

The main topic of the meeting was the discussion of the NBO-Q Microscopy Metadata Map. The Map aims to facilitate the distribution of responsibilities among WGs regarding the documentation of Microscope Hardware, Acquisition Settings, and Quality Control procedures. Caterina presented the schema she prepared and received feedback. As a result of the feedback, the map was updated. The current version of the map can be found here: https://nextcloud.quarep.org/index.php/s/E3AKjNMbWgXDN3B

Meeting documentation

20th meeting, 20th of February 2023

Meeting date

20/02/2023 @ 5:00 PM

Meeting summary

During the meeting we discussed the following items: 1) Next meeting will be held on March 20th 2023 and then we will continue every two months on the 3rd Monday. 2) Reminders will be sent 1 month, 1 week, 1 day, and 1 hour before each meeting. 3) The work of the WG will continue to concentrate on revising the 4DN-BINA-OME Microscopy Metadata Model and, as much as possible, will attempt to maintain compatibility with REMBI as a high-level set of recommendations. 4) WG7 works to collect the requirements of all WGs and create a consensus that incorporates the metadata requirements of all other WGs. As such WG7 works as an underlying platform on which all other WGs can build. It is important that we do a better job to explain to the QUAREP’s community that our work should be conceived as spanning across multiple WGs. 5) We need a general map of all components of the model, how they relate to each other, and which is the responsibility of which WGs 6) WG7 would like to have time during the annual meeting to discuss with everyone on this!

Meeting documentation

Subgroup Model, 5th meeting, 6th of February 2023

Meeting date

06/02/2023 @ 5:00 PM

Meeting summary

Discussion concerned primarily on review of current model revision activities and how to best handle the proposal/review/acceptance/implementation process when faced with the need to revise the NBO-Q model. Consensus: At the moment we are volunteer-driven and changes will have to be done on the basis of individuals taking the lead, driving a revision, putting together a revision and then submitting to the rest of the group for review, acceptance and implementation In this context, when a team of individuals is putting lots of work in making changes and they request feedback it would be great if people would take into account the amount of work that was done and be respectful Going forward we will need a formal method to propose/review/accept/implement changes to the model as the current model is not going to work for developers [a rough estimate would indicate that10000 hours of development are going to be needed for each model request for-change) RE: Camera model revision to increase efficiency concentrate on producing minimal description for each field and in a second round work on a more extensive glossary

Meeting documentation

19th meeting, 19th of December 2022

Meeting date

19/12/2022 @ 5:00 PM

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Subgroup Model, 4th meeting, 5th of December 2022

Meeting date

05/12/2022 @ 5:00 PM

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Subgroup Storage, 12th meeting, 29th of November 2022

Meeting date

29/11/2022 @ 4:00 PM

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Working Group 8

10th meeting, 7th of January 2021

Meeting date

07/01/2021 @ 4:00 PM

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9th meeting, 21st of December 2020

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8th meeting, 14th of December 2020

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7th meeting, 10 of December 2020

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6th meeting, 1st of December 2020

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5th meeting, 19th of November 2020

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Working Group 9

22nd meeting, 7th of March 2023

Meeting date

07/03/2023 @ 4:00 PM

Meeting documentation

21st meeting, 7th of February 2023

Meeting date

07/02/2023 @ 4:00 PM

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20th meeting, 6th of December 2022

Meeting date

06/12/2022 @ 4:00 PM

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19th meeting, 3rd of November

Meeting date

03/11/2022 @ 4:00 PM

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18th meeting, 6th of October 2022

Meeting date

06/10/2022 @ 4:00 PM

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17th meeting, 1st of September 2022

Meeting date

01/09/2022 @ 4:00 PM

Meeting documentation

Working Group 10

27th meeting, 14th of March 2023

Meeting date

14/03/2023 @ 4:00 PM

Meeting summary

For this meeting, we will need to take a decision about SBR parameter and all over parameter we decided not to consider. + 10 min per sub group to discuss briefly the progresses that have been made.

Meeting documentation

26th meeting, 14th of February 2023

Meeting date

14/02/2023 @ 4:00 PM

Meeting summary

For our second meeting of 2023, we are going to discuss about SBR definition and Image Resolution Estimation (IRE) parameters.

Meeting documentation

25th meeting, 17th of January 2023

Meeting date

17/01/2023 @ 4:00 PM

Meeting summary

For our first meeting of 2023, let’s just take 10 min per sub group to discuss briefly the progresses that have been made. And happy new year of course 🙂

Meeting documentation

24th meeting, 13th of December 2022

Meeting date

13/12/2022 @ 4:00 PM

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

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

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

Working Group 11

21st meeting, March 23rd 2023

Meeting date

24/03/2023 @ 12:00 AM

Meeting summary

1-We will review the Bare Minimal Requirements Checklist for “Methods” journals. You can all review it here: https://nextcloud.quarep.org/index.php/s/544SCiDkKHns9rj
2-We are also switching gears and will continue with the WG11 mission, which as you all know will include more comprehensive requirements. Below, please find the link to the document we will be working with today.

Meeting documentation

20th meeting, February 23rd 2023

Meeting date

23/02/2023 @ 10:51 AM

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

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

Meeting documentation

15th meeting, 30th of November 2022

Meeting date

30/11/2022 @ 5:00 PM

Meeting documentation