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Working Group 1

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

21st meeting, 3rd of August 2022

Meeting date

08/03/2022 @ 5:00 PM

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

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

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

Working Group 2

24th meeting, 14th of November 2022

Meeting date

14/11/2022 @ 5:00 PM

Meeting documentation

23rd meeting, 10th of October 2022

Meeting date

10/10/2022 @ 5:00 PM

Meeting documentation

22th meeting, 12th of September 2022

Meeting date

12/09/2022 @ 5:00 PM

Meeting summary

The camera metadata (WG2 + 7) group needs to work on a glossary, explaining the terminology used. It was decided that people from the camera subgroup will start working on this glossary. Furthermore, it was decided that we need to start thinking about the next microscope parts, for which the metadata structure and vocabulary can be standardized. Kees reported further on testing of the Quantiflash standardized light source. A continuous (DC) mode should be implemented in addition to the pulsed mode. The standardized light source will be discussed in detail during the November meeting. Personal learning sessions for Protocols.io will be offered to interested members of WG2.

Meeting documentation

21st meeting, 11th of July 2022

Meeting date

11/07/2022 @ 5:00 PM

Meeting documentation

20th meeting, 13th of June 2022

Meeting date

13/06/2022 @ 5:00 PM

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19th meeting, 9th of May 2022

Meeting date

19/05/2022 @ 5:00 PM

Meeting documentation

Working Group 3

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

15th meeting, 8th of September 2022

Meeting date

08/09/2022 @ 5:00 PM

Meeting documentation

14th meeting, 21st of July 2022

Meeting date

21/07/2022 @ 5:00 PM

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13th meeting, 23rd of June 2022

Meeting date

23/06/2022 @ 5:00 PM

Meeting documentation

12th meeting, 12 of May 2022

Meeting date

12/05/2022 @ 5:00 PM

Meeting documentation

Working Group 4

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

18th meeting, 21st of June 2022

Meeting date

21/06/2022 @ 5:00 PM

Meeting documentation

17th meeting, 17th of May 2022

Meeting date

17/05/2022 @ 5:00 PM

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16th meeting, 19th of April 2022

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15th meeting, 15th of March 2022

Meeting date

15/03/2022 @ 5:00 PM

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Working Group 5

23rd meeting, 10th of November

Meeting date

10/11/2022 @ 3:30 PM

Meeting documentation

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

Meeting documentation

20th meeting, 9th of June 2022

Meeting date

09/06/2022 @ 3:30 PM

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19th meeting, 12th of May 2022

Meeting date

12/05/2022 @ 3:30 PM

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18th meeting, 7th of April 2022

Meeting date

07/04/2022 @ 3:30 PM

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Working Group 6

16th meeting, 14th of September 2022

Meeting date

14/09/2022 @ 4:00 PM

Meeting documentation

15th meeting, 13th of July 2022

Meeting date

13/07/2022 @ 4:00 PM

Meeting documentation

14th meeting, 8th of June 2022

Meeting date

08/06/2022 @ 4:00 PM

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13th meeting, 27th of April 2022

Meeting date

27/04/2022 @ 4:00 PM

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12th meeting, 9th of March 2022

Meeting date

09/03/2022 @ 4:00 PM

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11th meeting, 9th of February 2022

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Working Group 7

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

Meeting date

05/12/2022 @ 5:00 PM

Meeting documentation

18th meeting, 21st of November 2022

Meeting date

21/11/2022 @ 5:00 PM

Meeting summary

Caterina reported that all the to-do items from last meeting have been completed. Created a granular task list based on what are tasks identified in each of the Sub-Groups and a link to spreadsheet was added to WG7 mainpage. In addition a proposal was tabled to announce QUAREP-WG7 meetings on Image.sc and it was agreed at the meeting. Ken reported the OME-Meeting on Metadata. Josh’s talk can be found here https://www.openmicroscopy.org/events/ome-community-meeting-2022/ · Great material for advocating about the need of a NG Metadata framework, although no clear definition of storage location. There were much discussion of Nature Methods and Nature Cell Biology request to QUAREP-LiMi to develop a light microscopy checklist for Nature Portfolio. Caterina reported back that we had initial meeting with Rita and Melina to discuss Nature requirements and initial meeting with WG7, 9, 11 and 12 chairs to dicuss next steps. We aim to provide the checklist by Christmas to Nature Methods. Nature is not going to release the data, but something that they will like to work and discuss with their editors.

Meeting documentation

Subgroup Model, 3rd meeting, 7th of November 2022

Meeting date

07/11/2022 @ 4:00 PM

Meeting summary

  1. Report back from Mathias and Caterina revision of the Camera Metadata Model based on the feedback from the JOINT CAMERA FEEDBACK GROUP Caterina and Mathias have completed the revision of the DETECTION SYSTEM 2022-10-07_NBO-Q_DETECTOR_v3-00-0_DRAFT_V01 spreadsheet (https://docs.google.com/spreadsheets/d/1KQgAClf4lp90sZ0egUez1h2HYwhvC5VFbaBn1mqvgqE/edit?usp=sharing) Caterina and Mathias have worked at testing LinkML as a framework that we could use to represent the metadata model and would allow the automatic generation of different representations starting from a unique source of truth. · Specifically the advantage of LinkML is that it can use a spreadsheet as the source of truth · The spreadsheet has to be following the schemasheet format (https://linkml.io/schemasheets/) o https://docs.google.com/spreadsheets/d/1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ/edit#gid=55566104 · Mathias and Caterina are testing the schemasheet format to see if it can be used as a source of truth
  2. Decide on more frequent schedule for follow up meetings · Mathias and Caterina will communicate when the schemasheet version of NBO-Q v3.00_DRAFT is ready to be discussed and presented · David, Mathias, Roland, and Britta will review the 2022-10-07_NBO-Q_DETECTION SYSTEM_v3-00-0_DRAFT_V01 spreadsheet (https://docs.google.com/spreadsheets/d/1KQgAClf4lp90sZ0egUez1h2HYwhvC5VFbaBn1mqvgqE/edit?usp=sharing) so that we can then present it to the CAMERA FEEDBACK GROUP to finalize the request for changes and produce a DRAFT v02 that can be used as a source of truth for implementation

Meeting documentation

Subgroup Capture Tools, 6th meeting, 17th of October 2022

Meeting date

17/10/2022 @ 4:00 PM

Meeting documentation

Subgroup Model 2nd Meeting, 5th of October 2022

Meeting date

05/10/2022 @ 4:00 PM

Meeting summary

–Caterina and Mathias are having a series of twice-a-week in-person meetings at UMass Med to produce a revised version of the NBO-Q model Excel Spreadsheet that incorporates all proposals for change that emerged from the series of meetings with Camera Manufacturers (referred to as JOINT CAMERA FEEDBACK GROUP) The product should be done in 1 month. –This revised spreadsheet will be used as a starting point for our work as well as to solicit a final round of feedback from the JOINT CAMERA FEEDBACK GROUP. –We will use LinkML as the framework to represent the metadata model. LinkML core format is YAML but a SPREADSHEET can be used as the core representation from which other representations can be generated. DECISIONS: NEXT MEETING ON 11/7/2022 AT 11 am ET and then every 1st Monday after that LinkML will be tested to support the production of different interlinked representations of the model

Meeting documentation

Subgroup Storage, 11th meeting, 27th of September 2022

Meeting date

27/09/2022 @ 4:00 PM

Meeting documentation

Working Group 8

10th meeting, 7th of January 2021

Meeting date

07/01/2021 @ 4:00 PM

Meeting documentation

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

20th meeting, 6th of December 2022

Meeting date

06/12/2022 @ 4:00 PM

Meeting documentation

19th meeting, 3rd of November

Meeting date

03/11/2022 @ 4:00 PM

Meeting documentation

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

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16th meeting, 7th of July 2022

Meeting date

07/07/2022 @ 4:00 PM

Meeting documentation

15th meeting, 5th of May 2022

Meeting date

05/05/2022 @ 4:00 PM

Meeting documentation

Working Group 10

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

21st meeting, 12th of July 2022

Meeting date

12/07/2022 @ 4:00 PM

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20th meeting, 14th of June 2022

Meeting date

14/06/2022 @ 4:00 PM

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19th meeting, 10th of May 2022

Meeting date

10/05/2022 @ 4:00 PM

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18th meeting, 22nd of February 2022

Meeting date

22/02/2022 @ 4:30 PM

Meeting documentation

Working Group 11

14th meeting, 27th of October 2022

Meeting date

27/10/2022 @ 5:00 PM

Meeting documentation

13th meeting, 22nd of September 2022

Meeting date

22/09/2022 @ 5:00 PM

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12nd meeting, 25th of August 2022

Meeting date

25/08/2022 @ 5:00 PM

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11th meeting, 26th of May 2022

Meeting date

26/05/2022 @ 5:00 PM

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10th meeting, 28th of April 2022

Meeting date

28/04/2022 @ 5:00 PM

Meeting documentation

9th meeting, 24th of March 2022

Meeting date

24/03/2022 @ 4:00 PM

Meeting documentation