WG 1 – Illumination power

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.

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.

We had a smaller group of 14 participants to the 20^th 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).

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.

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 1^st, 5pm CEST. Looking forward to seeing you all there again!

We had a total of 23 members attending. We summarized some information shared at the joint WG9 and co-chair held on March 3^rd. 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 4^th.

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.

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 16^th WG1 meeting to be held on Wednesday March 2^nd, 17:00-18:30 CET).

We discussed privacy consideration for the data uploaded to the AirTable WG1 database and will discuss further with WG9 and AirTable the different options to limit visibility and access. We also finalized the main document, discussed the linearity protocol and adding more representative data. The protocol has been transferred to Protocol.io in a private account, it will be further updated and made accessible to all QUAREP members early next year. We also assigned the different appendices to different subgroups to work on a very first, publishable version of the power meter settings, automation measurements, impact of environmental factors, and troubleshooting sections.

We had 20 participants today and welcomed 3 new members. We presented Airtable, a new web-based platform for shared database. All previously collected data and new plots can be found on this Dashboard. Use the following Form  to enter new data. You will need to sign in and create an account before getting access. We also reviewed very briefly some editing done by Laurent and Nathalie on the main document (formatting and reorganization) and a new draft version of the protocol uploaded on Protocol.io. Finally, we went over some example data of laser warming up presented by Laszlo. We all agreed that it should be included in our protocol.