Working Group 1
21st meeting, 3rd of August 2022
Meeting date
08/03/2022 @ 5:00 PM (CET/CEST)
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.
20th meeting, 6th of July 2022
Meeting date
06/07/2022 @ 5:00 PM (CET/CEST)
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:
- 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.
- 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
- 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).
19th meeting, 1st of June 2022
Meeting date
01/06/2022 @ 5:00 PM (CET/CEST)
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:
- 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.
- 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.
18th meeting, 4th of Mai 2022
Meeting date
04/05/2022 @ 5:00 PM (CET/CEST)
Meeting summary
Quick reminder of WG1 next priorities, based on the votes of WG1 members:
- Extend the protocol to other microscopy modalities (wide-field microscope – LED, Arc-Lamps, lasers)
- Extend the protocol to different laser types (i.e. multiphoton)
- Extend the protocol to other laser-based modalities : (TIRF, SIM, light sheet)
- 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
- Extension of Power Meter Q&A (Led by Manfred mgonnert@thorlabs.com)
- Metadata/Definition specific to WG1 (Led by Britta schroth@mpi-cbg.de & David david.grunwald@umassmed.edu)
17th meeting, 6th of April 2022
Meeting date
06/04/2022 @ 5:00 PM (CET/CEST)
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:
- Extend the protocol to other microscopy modalities (wide-field microscope – LED, Arc-Lamps, others)
- Extend the protocol to different laser types (i.e. multiphoton)
- Extend the protocol to other laser-based modalities (TIRF, SIM, light sheet)
- Validation from the public: BioImaging North America (BINA) will be using our protocol in their Metrology Suitcase program.
- Translation of the protocol: BINA will also translate the protocol into French and Spanish for Canada and Mexico participants in the Metrology Suitcase program.
- A common Glossary will be created for all WGs (WG7 and WG9 will lead this effort)
- Extension of the automation section (Lead by Miso and Nasser)
- Extension of Power Meter Q&A (Lead by Manfred)
- Metadata/Definition specific to WG1 (Britta & David)
- Others? (we need volunteers to lead other sub-WG1s)
16th meeting, 2nd of March 2022
Meeting date
02/03/2022 @ 5:00 PM (CET/CEST)
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.
Working Group 2
25th meeting, 12th of December 2022
Meeting date
12/12/2022 @ 5:00 PM (CET/CEST)
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.
24th meeting, 14th of November 2022
Meeting date
14/11/2022 @ 5:00 PM (CET/CEST)
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.
23rd meeting, 10th of October 2022
Meeting date
10/10/2022 @ 5:00 PM (CET/CEST)
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.
22th meeting, 12th of September 2022
Meeting date
12/09/2022 @ 5:00 PM (CET/CEST)
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.
Working Group 3
Working Group 4
19th meeting, 20th of September 2022
Meeting date
20/09/2022 @ 5:00 PM (CET/CEST)
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.
Working Group 5
Working Group 6
Working Group 7
Subgroup Model, 6th meeting, 6th of March 2023
Meeting date
06/03/2023 @ 5:00 PM (CET/CEST)
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
20th meeting, 20th of February 2023
Meeting date
20/02/2023 @ 5:00 PM (CET/CEST)
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!
Subgroup Model, 5th meeting, 6th of February 2023
Meeting date
06/02/2023 @ 5:00 PM (CET/CEST)
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
