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Working Group 1

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20th meeting, 6th of July 2022

Meeting date

06/07/2022 @ 5:00 PM

Meeting summary

We had a smaller group of 14 participants to the 20th meeting. Nevertheless, we had once again a productive discussion and made some progress reviewing our version 2 of the protocol and made additions and changes to step 2 and 3 to include widefield microscope illumination. We also heard progress made from our subgroups:
  1. Extension of the automation section (Led by Miso mitkovski@em.mpg.de and Nasser ndarwish@ist.ac.at): new members joined (Chloe and Rodrigo) and the group is now testing and integrating the automation script (for both acquisition and analysis) with data management using AirTable.
  2. Extension of Power Meter Q&A (Led by Manfred mgonnert@thorlabs.com ): a new appendix (1b) has been created on how to measure power of broadband light sources. Please review on Protocol.io here
  3. Metadata/Definition specific to WG1 (Led by Britta schroth@mpi-cbg.de  & David david.grunwald@umassmed.edu): still working on the WG2 camera glossary (the plan is to get as many companies involved as possible).

Meeting documentation

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19th meeting, 1st of June 2022

Meeting date

01/06/2022 @ 5:00 PM

Meeting summary

During this meeting, we made good progress on our version 2 of the protocol, extending microscopy modalities to wide-field imaging. We also have a re-actualized AirTable form and fields. We also heard progress made in our subgroups:
  1. Extension of the automation subgroup had a meeting. The recording can be found here. A new tutorial video on how to install and use the automation macro while using Nikon NIS element and the Thorlab power meter software has been created. You can find it here.
  2. The power meter Q&A is being extended to include information about LED light source. Please contact Manfred mgonnert@thorlabs.com if you would like to contribute.
We also had an extensive discussions on pulsed lasers, on the technology behind LEDs, and the inherent lack of stability of arc lamps. Finally, we completed our recommendations for the warm-up step for all light sources and used the step case function of Protocols.io to highlight differences.

Meeting documentation

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18th meeting, 4th of Mai 2022

Meeting date

04/05/2022 @ 5:00 PM

Meeting summary

Quick reminder of WG1 next priorities, based on the votes of WG1 members:
  1. Extend the protocol to other microscopy modalities (wide-field microscope – LED, Arc-Lamps, lasers)
  2. Extend the protocol to different laser types (i.e. multiphoton)
  3. Extend the protocol to other laser-based modalities : (TIRF, SIM, light sheet)
This month we reviewed the metadata fields needed for Wide-field microscope – LED, Arc-Lamps, and others light source in AirTable Dashboard and adjusted our Form. Report from our subgroups were minimal. The Automation subgroup is planning to meet, see below. Please contact the lead of the subgroup you would like to contribute to.
  1. Extension of the automation section (led by Miso mitkovski@em.mpg.de & Nasser ndarwish@ist.ac.at). Next Monday (05/09) 17:00 CET, the automation subgroup will meet. Kees will present his latest macros. https://zoom.us/j/97497511867; Meeting ID: 974 9751 1867; Passcode: 445833
  2. Extension of Power Meter Q&A (Led by Manfred mgonnert@thorlabs.com)
  3. Metadata/Definition specific to WG1 (Led by Britta schroth@mpi-cbg.de  & David david.grunwald@umassmed.edu)
Finally, we briefly discussed the possibility of using the Step Care function in Protocols.io template to add specific recommendations for the different Microscopy modalities and light sources. See example already created in the new version 2 of the protocol on protocols.io. The private new version of the protocol can be found here. Our next meeting will be on Wednesday June 1st, 5pm CEST. Looking forward to seeing you all there again!

Meeting documentation

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17th meeting, 6th of April 2022

Meeting date

06/04/2022 @ 5:00 PM

Meeting summary

We had a total of 23 members attending. We summarized some information shared at the joint WG9 and co-chair held on March 3rd. We reviewed feedback received at this meeting on our “Lesson’s learned” presentation. Borrowing David Grunwald’s words here: “WG1 has received highest praise and is seen as the poster child success story for QuaRep. WG1 has delivered greatly and is noticed. Everyone here should take a moment and enjoy, we clearly did a very good job.” On the same slide you will find the Protocols.io stats on the impact of our protocol with a total of 400 views for the month on March. We also reviewed the results of the survey. Based on the votes of WG1 participants, the next priorities of WG1 will be the following:
  1. Extend the protocol to other microscopy modalities (wide-field microscope – LED, Arc-Lamps, others)
  2. Extend the protocol to different laser types (i.e. multiphoton)
  3. Extend the protocol to other laser-based modalities (TIRF, SIM, light sheet)
We also discussed that we may get the following by collaborating with other groups:
  1. Validation from the public: BioImaging North America (BINA) will be using our protocol in their Metrology Suitcase program.
  2. Translation of the protocol: BINA will also translate the protocol into French and Spanish for Canada and Mexico participants in the Metrology Suitcase program.
  3. A common Glossary will be created for all WGs (WG7 and WG9 will lead this effort)
We will also have subgroups working on specific topics:
  1. Extension of the automation section (Lead by Miso and Nasser)
  2. Extension of Power Meter Q&A (Lead by Manfred)
  3. Metadata/Definition specific to WG1 (Britta & David)
  4. Others? (we need volunteers to lead other sub-WG1s)
Finally, we created a private new version of the protocol on protocols.io and started adapting the protocol to widefield and LED light source working on the first two steps of the protocol. Our next meeting will be on Wednesday May 4th.

Meeting documentation

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16th meeting, 2nd of March 2022

Meeting date

02/03/2022 @ 5:00 PM

Meeting summary

We had a great debriefing session about lesson’s learned over the past year and from publishing our first version of our protocol at protocol.io. We have created a document that will be shared with all co-chairs and WG9 of QUAREP-LiMi. We have also started a list of future tasks for WG1, please continue adding to it here. A survey will be sent out next week.

Meeting documentation

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15th meeting, 3rd 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).

Meeting documentation

Working Group 2

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20th meeting, 13th of June 2022

Meeting date

13/06/2022 @ 5:00 PM

Meeting documentation

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19th meeting, 9th of May 2022

Meeting date

19/05/2022 @ 5:00 PM

Meeting documentation

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18th meeting, 11th of April 2022

Meeting date

11/04/2022 @ 5:00 PM

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.

Meeting documentation

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17th meeting, 14th of March 2022

Meeting date

14/03/2022 @ 5:00 PM

Meeting documentation

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16th meeting, 14th of February 2022

Meeting documentation

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15th meeting, 10th of January 2022

Meeting documentation

Working Group 3

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12th meeting, 12 of May 2022

Meeting date

12/05/2022 @ 5:00 PM

Meeting documentation

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11th meeting, 21st of April 2022

Meeting date

21/04/2022 @ 5:00 PM

Meeting documentation

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10th meeting, 24th of March 2022

Meeting date

24/03/2022 @ 5:00 PM

Meeting documentation

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9th meeting, 10th of February 2022

Meeting documentation

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8th meeting, 13th of January 2022

Meeting documentation

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7th meeting, 9th of December 2021

Meeting documentation

Working Group 4

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18th meeting, 21st of June 2022

Meeting date

21/06/2022 @ 5:00 PM

Meeting documentation

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17th meeting, 17th of May 2022

Meeting date

17/05/2022 @ 5:00 PM

Meeting documentation

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16th meeting, 19th of April 2022

Meeting documentation

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15th meeting, 15th of March 2022

Meeting date

15/03/2022 @ 5:00 PM

Meeting documentation

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14th meeting, 11th of March 2022

Meeting date

11/03/2022 @ 10:30 AM

Meeting documentation

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13th meeting, 18th of January 2022

Meeting documentation

Working Group 5

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20th meeting, 9th of June 2022

Meeting date

09/06/2022 @ 3:30 PM

Meeting documentation

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19th meeting, 12th of May

Meeting date

12/05/2022 @ 3:30 PM

Meeting documentation

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18th meeting, 7th of April 2022

Meeting date

07/04/2022 @ 3:30 PM

Meeting documentation

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17th meeting, 10th of March 2022

Meeting date

03/03/2022 @ 3:30 PM

Meeting documentation

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16th meeting, 10th of February 2022

Meeting documentation

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15th meeting, 16th of December 2021

Meeting documentation

Working Group 6

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14th meeting, 8th of June 2022

Meeting date

08/06/2022 @ 4:00 PM

Meeting documentation

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13th meeting, 27th of April 2022

Meeting date

27/04/2022 @ 4:00 PM

Meeting documentation

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12th meeting, 9th of March 2022

Meeting date

09/03/2022 @ 4:00 PM

Meeting documentation

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11th meeting, 9th of February 2022

Meeting documentation

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10th meeting, 12th of January

Meeting documentation

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9th meeting, 8th of December 2021

Meeting summary

https://bwsyncandshare.kit.edu/f/1703353969

Working Group 7

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15th meeting, 20th of June 2022

Meeting date

20/06/2022 @ 5:00 PM

Meeting documentation

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14th meeting, 16th of May 2022

Meeting date

16/05/2022 @ 5:00 PM

Meeting documentation

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13th meeting, 21st of March 2022

Meeting date

21/03/2022 @ 5:00 PM

Meeting documentation

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12th meeting, 21st of February 2022

Meeting date

21/02/2022 @ 5:00 PM

Meeting summary

In this meeting we discussed:
  1. Revision of the WG7 main webpage on QUAREP.org
  2. Review progress done with WG2 to revise the Camera section of 4DN-BINA-OME-(QUAREP) Microscopy Metadata model in collaboration with Camera manufacturers and members of the Camera community.
  3. Review progress of SubGroup 2 (Metadata Education) and SubGroup 3 (Metadata Storage Specifications).
  4. Reminder: the novel SubGroup 4 (Model Revision) was formed but it did not convene yet because they are waiting for the end of the first phase of Camera community conversations. Please join us in this important work.

Meeting documentation

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11th meeting, 17th of January 2022

Meeting documentation

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10th meeting, 15th of November 2021

Meeting documentation

Working Group 8

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10th meeting, 7th of January 2021

Meeting date

07/01/2021 @ 4:00 PM

Meeting documentation

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9th meeting, 21st of December 2020

Meeting documentation

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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

Meeting documentation

Working Group 9

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15th meeting, 5th of May 2022

Meeting date

05/05/2022 @ 4:00 PM

Meeting documentation

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14th meeting, 5th of April 2022

Meeting date

05/04/2022 @ 4:00 PM

Meeting documentation

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13th meeting, 3rd of March 2022

Meeting date

03/03/2022 @ 4:00 PM

Meeting documentation

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12th meeting, 1st of February 2022

Meeting documentation

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11th meeting, 7th of December 2021

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10th meeting, 2nd of November 2021

Meeting documentation

Working Group 10

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20th meeting, 14th of June 2022

Meeting date

14/06/2022 @ 4:00 PM

Meeting documentation

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19th meeting, 10th of May 2022

Meeting date

10/05/2022 @ 4:00 PM

Meeting documentation

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18th meeting, 22nd of February 2022

Meeting date

22/02/2022 @ 4:30 PM

Meeting documentation

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17th meeting, 25th of January 2022

Meeting documentation

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16th meeting, 14th of December 2021

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15th meeting, 23rd of November 2021

Meeting documentation

Working Group 11

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10th meeting, 26th of May 2022

Meeting date

26/05/2022 @ 5:00 PM

Meeting documentation

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9th meeting, 28th of April 2022

Meeting date

28/04/2022 @ 5:00 PM

Meeting documentation

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8th meeting, 24th of February 2022

Meeting date

24/02/2022 @ 5:00 PM

Meeting documentation

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7th meeting, 27th of January 2022

Meeting documentation

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6th meeting, 23rd of September 2021

Meeting documentation

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5th meeting, 21st of July 2021

Meeting documentation