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WG 2 – Detection system performance

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WG 2 – Objectives

WG2 focuses on the detection system, comprising the detection path and its detector(s), and how it measures the signal from the sample.

Members of WG2 aim to standardize the characterization of the detection system performance and create standard procedures for monitoring it over time, thereby revealing performance issues that could affect data reproducibility. Therefore, WG2 will define universal, externally measurable parameters applicable to any type of detector (e.g., photons, linearity, noise), together with measurement tools and protocols for measuring these parameters from common detector types. These universal parameters will be specified according to each distinct type of detector’s internal parameters, which have already been defined by the community. They will enable the evaluation and comparison of different detection systems, thus pinpointing the most suitable technology for given applications.

WG 2 – Co-Chairs

WG 2 - Latest News

Illumination Stability and Linearity Measurement Protocol V.3

WG 1 - Illumination Power published its third version of the protocol "Illumination Power, Stability and Linearity Measurements for Confocal, Widefield and Multiphoton Microscopes". The protocol is featured on protocols.io

QUAREP-LiMi welcomes our first member from Thailand

We are delighted to warmly welcome our first member from Thailand, Dr Tassanee Lerksuthirat from the Research Center Ramathibodi Hospital just joined Working Group 1, 7, 8, 10, 11 and 12 of QUAREP-LiMi.

Illumination Stability and Linearity Measurement Protocol V.2 has been published

WG 1 - Illumination Power published its second version of the protocol "Illumination Power, Stability and Linearity Measurements for Confocal and Widefield Microscopes". The protocol is featured on protocols.io

 

Last meeting: 14th April 2025, 5:00 pm

Release of protocols collection:

 
 
  1. Subgroup: Area detector
    • Aims: Establish protocols for characterization of detection systems with an area detector.
    • Co-leads: Britta Schroth, David McFadden
    • Contact information: schroth@mpi-cbg.de
    • On-going tasks: 
      • Move measurement protocol to protocols.io
      • Test measurement protocol with marker pen as sample
      • Evaluate measurement and analysis parameters written down in Airtable
    • Cloud storage location (can be accessed as a member) → here
  2. Subgroup: Point detector
    • Aims: Establish protocols for characterization of detection systems with a point detector.
    • Co-leads: Gert-Jan Bakker, Andre Zeug
    • Contact information: gert-jan.bakker@radboudumc.nl
    • On-going tasks: 
      • Insert measurement protocol to protocols.io
      • Generate comments and hints for protocol
      • Evaluate measurement and analysis parameters written down in Airtable
    • Cloud storage location (can be accessed as a member) → here
  3. Subgroup: Test sample
    • Aims: investigate and define standardized samples for characterization of detection systems.
    • Co-leads: Valeria Berno, David McFadden
    • Contact information: berno.valeria@hsr.it
    • On-going tasks: 
      • Test and characterize standardized light sources for characterization of microscope’s detection systems.
    • Cloud storage location (can be accessed as a member) → here
  4.  

51st meeting, 14th of April 2025

Meeting date

14/04/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

50th meeting, 10th of March 2025

Meeting date

10/03/2025 @ 5:00 PM (CET/CEST)

Meeting summary

Agenda points

  1. Organizational matters and News
  2. Annual QUAREP-LiMi meeting
  3. ELMI 2025 workshop contribution
  4. Update on NBO-Q camera model & glossary
  5. Next steps

Meeting documentation

49th meeting, 10th of February 2025

Meeting date

10/02/2025 @ 5:00 PM (CET/CEST)

Meeting summary

This was our first meeting since the publication of our WG2 Protocols collection. Therefore, our main focus was to discuss the next steps for our work. 
We agreed on a key concern: how to collect data now that the protocol is available, and how we can assist users in automating the data collection process for use with the analysis tool. We agreed to use OMERO as our main tool. However, this will require significant work. We need to have an easy way to upload data to the OMERO server. Secondly, we need to determine the metadata necessary to support the main detector parameters that can be analysed using our published protocol tools.
Secondly, we got an update on the progress of the Camera Glossary and Model work. The hardware part is almost done. This will be followed by working on the settings part.
Finally, we decided to use the exciting possibility to present our Protocols collection by offering one or two workshops in the community room during the ELMI meeting in June 2025 in Heidelberg.

Meeting documentation

48th meeting, 13th of January 2025

Meeting date

13/01/2025 @ 5:00 PM (CET/CEST)

Meeting summary

After the usual short organisational matters and news section, we started right away with an overview over the work done on our protocols collection since the last meeting.
There have been done updates to the figures and figure legends, and all links have been checked and updated. All authors gave their consent to their respective authorship, author order, and listed contributions. Author contributions and funding are listed in each protocol via two respective pdfs in the acknowledgment section. In addition, we looked at an example protocol run including how to add comments, to see the difference between viewing a protocol versus running it.
Subsequently, we went through the collection and all protocols to have a last check of the respective content. Several small but significant changes were made. An exhaustive list of this changes can be found in our meeting minutes. We agreed to collect and save all images and figures used for the protocols on the QUAREP-LiMi cloud. A folder will be set up for this in the WG2 work done folder.
At 6:20 PM we did publish our protocols collection. You can find the titles and DOI links below.
After this great achievement we had the pleasure of welcoming our new member Nicolas Stifani from Montreal.
For finalising our other current major project, the NBO-Q camera model and glossary, there are four meetings scheduled in January. There will be a detailed report about this project in the February meeting. In addition, in the next meeting we will take time to discuss the next steps and goals for our future WG2 work.
Collection:
Characterization of the Photon Conversion Factor, Noise, and Dynamic Range of Light Microscope Detection Systems
Separate protocols:

1. Introduction – Background and Aims

DOI: dx.doi.org/10.17504/protocols.io.eq2lyw5mevx9/v1

2. Sample Preparation – An Easy-to-Prepare Sample Slide

DOI: dx.doi.org/10.17504/protocols.io.x54v92b91l3e/v1

3. Data Generation – Systems with an Area Detector

DOI: dx.doi.org/10.17504/protocols.io.bp2l62eorgqe/v1

4. Data Generation – Systems with a Point Detector

DOI: dx.doi.org/10.17504/protocols.io.j8nlk8176l5r/v1

5. Analysis – Characterization of the Photon Conversion Factor, Noise, and Dynamic Range

DOI: dx.doi.org/10.17504/protocols.io.rm7vzjew2lx1/v1

Meeting documentation

47th meeting, 9th of December 2024

Meeting date

09/12/2024 @ 5:00 PM (CET/CEST)

Meeting summary

We started the meeting with a short discussion about our meeting day, time, and length of the meeting. In the end we decided to keep the current scenario of meeting each second Monday of a month for 90mins from 5:00 – 6:30 PM CET. This discussion was followed by a short report from the last two QUAREP-LiMi SC meetings. The main message for us was that the SC approved of our request to publish our protocols collection. This approval included the conditions that we solve all open comments and clarify author contributions following the CreDiT taxonomy. It was suggested to us to add a document to each protocol with the respective author’s contribution list. The reminder of the meeting we used to go through the comments at the collection, the protocol 1. introduction, had a quick look at the protocol 2. – Sample Preparation, and started going through the comments of protocol 3. Data Generation – Systems with Area Detector. Since there were quite a few very helpful last minute comments, we did not manage to finish going through the protocols. We are still aiming to finish and publish before the holiday season. Therefore, we decided to meet again this week Thursday, December 12th, from 4-5PM CET in the WG2 zoom room. Everybody is welcome to join.
At the end of the meeting we briefly talked about the current status of the NBO-Q camera model and glossary project. We finished the series of meetings revisiting the hardware part of the model after the first change updates. The latest changes are being added to the model. The debriefing group is working on preparing the settings part of the model. Another stakeholder meeting series will be organised for January 2025.
We closed the meeting by having a quick look at the list of To Do’s for next year.

Meeting documentation

46th meeting, 11th of November 2024

Meeting date

11/11/2024 @ 5:00 PM (CET/CEST)

Meeting summary

After the usual short organisational matters and news section, we started our meeting with the presentation by David Grunwald about his soon to be published MetaMax manuscript. MetaMax is a tool hat can be used for detector calibration. The main request from David is to check if there is any input from our WG2 work that needs to be acknowledged. You can find the manuscript and a document for your comments in our 46th meetings folder.
Next Britta presented a request from WG1 to review version 3 of its protocol on measuring illumination power and stability. Version 3 now contains also measurement requirements for multi-photon systems. In addition, it has an improved table of contents and its text was modified for clarity and accuracy. Please give comments, feedback, and endorsement directly in protocols.io until end of November.
The NBO-Q camera model ad glossary is planned to be finished by the end of this year. To achieve this, three new stake holder meeting dates were announced (Nov 11th, Nov 22nd, Dec 4th). A lock-in meeting to prepare the settings part is planned on Dec 4th. Please watch out for the invitation emails.
The main part of our meeting was again dedicated towards finalising our WG2 protocols collection. We got several helpful and positive comments from WG2 members and also members from other WGs. The most urgent comment was for us to clarify our aim 1. We discussed this and agreed on a version. For the reminder of the meeting we split into two break out rooms to work on the collection, protocols 1 (introduction) and 5 (analysis) in one room and protocols 2 (sample prep) and 3 and 4 (data collection) in the other room. Since we did not manage to finish, we agreed to have extra meetings to work on the protocols (see meeting minutes for exact dates and time). Our aim is to present the final collection to the steering committee on December 3rd for approval to publish.
Addendum: Britta presented our protocols collection draft during the SC meeting on November 12th. We got the OK to present our collection for publication approval in the December 3rd meeting. 

Meeting documentation

45th meeting, 14th of October 2024

Meeting date

14/10/2024 @ 5:00 PM (CET/CEST)

Meeting summary

We started the meeting with a brief report from the last steering committee meeting followed by a short report about the current status of the work at the NBO-Q camera model and glossary. The camera model work is progressing steadily. We aim to finish the hardware part first and then continue with the settings part. To prepare well for this, a small group will meet beginning of December. More stakeholder meetings will take place in October and November. The main part of our meeting was spent working on our protocols collection. By now we reserved the DOIs for later publication and sent emails to the co-chairs of the other WGs to ask for feedback. We discussed to also present during upcoming meetings of other WGs if possible and appropriate. We aim to publish the collection until the end of 2024. For that we need to either present in the SC meeting in November or December. Decision will be made in our November WG2 meeting. The reminder of the meeting we worked on our protocols collection going through the comments we already received there.

Meeting documentation

44th meeting, 9th of September 2024

Meeting date

09/09/2024 @ 5:00 PM (CET/CEST)

Meeting summary

After the summer break, the WG2 meeting was a good opportunity to redefine our deadlines for completing our protocol collection.
We discussed guidelines and disclaimers, the collection of new sample images, and formed small groups to finalize each protocol for sending out our collection for testing and comments to the whole QUAREP-LiMi community as soon as possible.
WG2, together with WG7, is also involved in finalizing the camera model and glossary part of the NBO-Q model schema. To conclude the revision process, we will hold three further meetings with the stake-holder group still this month.
The preparation of  both, the protocol collection as well as the NBO-Q camera model and glossary, is very important for achieving our next goal, the publication of our first paper.

Meeting documentation

43rd meeting, 8th of July 2024

Meeting date

08/07/2024 @ 5:00 PM (CET/CEST)

Meeting summary

Since we had previously decided to skip our regular WG2 August meeting, we agreed to use August for finalising our protocols. On August 19th we will meet at our usual WG2 time (5:00 – 6:30PM CEST) for a protocols collection hackathon. This discussion was followed by short reports from the QUAREP-LiMi SC meeting, from the Dutch microscopy association, and about a new QC white paper by evident. During the subsequent agenda point we talked about the next steps towards finalising the NBO-Q camera model and glossary. First final revision meetings by the stakeholder groups were planned for July.

The main agenda point of our 43rd meeting was discussing the next steps towards finalising our protocols for publication. We agreed on the following timeline: until August 19th finalise separate protocols, put them into one collection during the hackathon on August 19th, get the protocols collection tested theoretically and practically and collect example measurements until October 14th. Implement comments and example measurements until November 11th (our WG2 meeting) and present the final protocols collection to the QUAREP-LiMi steering committee on November 12th. To finalise our separate protocols, we formed four small teams who will organise respective discussion meetings. For this version of the protocols collection we decided to keep separate protocols for point and area detectors, respectively. We plan to add protocols based on the French QC paper in the next version of our protocols collection.

Meeting documentation

42nd meeting, 10th of June 2024

Meeting date

10/06/2024 @ 5:00 PM (CET/CEST)

Meeting summary

After agreeing to take a summer break and skip our August meeting, we discussed the QUAREP-LiMi workshop contributions to ELMI. One workshop was held by WG5 and the other one jointly by WG2 and WG13 members. Both workshops were well received. Several  questions were raised during our joined WG2-WG13 workshop and also during discussions afterwards. These need to be addressed when finalising our protocols. Discussing the steps and the timeline towards publishing our protocols was the next point on our meeting agenda. Participants reported from the meeting with Emma Ganley from protocols.io. Based on that we decided to best publish our protocols in form of a protocols collection. Smaller subgroups will work on the protocols until the July meeting. If need be, we will use the August meeting date for a dedicated protocols hackathon. We aim to present the finished collection to the QUAREP-LiMi steering committee in early fall.

Meeting documentation

Memberlist WG 2

Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy

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