WG 1 – Illumination power

We had a short round of presentation for new comers. We decided to pause just this time our work on our protocol and 2-photon microscopy modality to focus on irradiance, and had the pleasure to listen to two very nice presentations by Ronian Siew and then Alienor Lahlou. For those of you who missed it, the recordings can be found here.

We summarized the By-Laws’ presentation since everyone had seen it at least once. The by-laws and its accompanying documents (Code of Conduct – CoC, Terms of Reference – ToR, and Best Practices – BP) aim to ensure QUAREP-LiMi provides a diverse, equitable, inclusive and transparent environment for its community to gather, address and efficiently make decision to critical challenges. You can find previous recordings of the By-Laws presentation from WG2 here, as well as the slides here. In the folder named Decision Making Discussion https://nextcloud.quarep.org/index.php/f/445127 you will find the other relevant documents related to the by-laws: •BP_BestPractices for QUAREP-LiMi Operations.docx •CoC_WorkGroups.docx •Bylaws Draft_04_a.docx Here are our action items: 1.      WG1 needs to appoint one representative for the SC, ERB, and OB (two-year terms). 2.      WG1 needs to elect its co-chairs for the next two-year term. Nathalie and Laurent are happy to continue on for another two year. We would love to have a third co-chair. 3.      We need candidates! – Let us know if you are interested in being our WG1 representative for SC (ideally one of the co-chairs), ERB, or OB, or if you want to become a WG1 co-chair before March 12^th. We also briefly brainstormed on known ways to measure irradiance and decided that a path forward would be to review a proposed definition (by WG13) and present a manuscript (journal club style) at our next meeting. WG1 will meet again on the 3^rd of April and will then continue expanding the Illumination power stability protocol to multi-photons.

First, our collaboration with WG-13 has been defined. Philippe Laissue (co-chair of WG13) talked about the mission of WG13 and how a protocol on how to measure irradiance could fit within the guidance on phototoxicity. Our first goal will be to define irradiance and write a small paragraph to summarize existing methods and guidelines on irradiance. Please share all references you have in this folder or directly in Zotero. We will define irradiance and discuss papers found at our next WG1 meeting (30 min each month). We then briefly discussed Robert Lees very relevant preprint on bioRxiv. We also made headway with version 3 of our protocol and included multi-photons specific comments and recommendations to steps 4 to 6 when needed. We will continue with step 7 at our next meeting. Please go to the protocol online here and add your comments and suggestions to the first 6 steps of the protocol. We will discuss all new comments at our next meeting.

During this meeting, we branched version 2 of our protocole to extrend it to Multi-photon systems. We discussed and modified staps 1 to 3 of the protocol.

Lin Yangchen presented his protocol and tools for “Irradiance Measurement on a spinning-disk confocal and TIRF microscope”. We decided to extend next time our protocol to 2P microscopy modality, and we collected the names of people in WG1 who want to collaborate with WG13 to create protocols on irradiance measurement and assessment of phytotoxicity. If you want also to join this subgroup, please contact Natalie Gaudreault.

Andrii Repula, Product Support Engineer at Lumencor, presented his white paper and how they measure light source stability at his company.

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.

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.

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.