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

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

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.

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

 

Upcoming meeting: 13th October 2025, 5:00 pm
Last meeting: 8th September 2025, 5:00 pm

  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.  

55th meeting, 13th of October 2025

Meeting date

13/10/2025 @ 5:00 PM (CET/CEST)

Meeting documentation

54th meeting, 8th of September 2025

Meeting date

08/09/2025 @ 5:00 PM (CET/CEST)

Meeting summary

Agenda

  1. Organizational matters and News
  2. Update on NBO-Q camera model & glossary
  3. Updates after the summer break (paper, automation…)
  4. Decide on next priorities

Meeting documentation

53rd meeting, 23rd of June 2025

Meeting date

23/06/2025 @ 5:00 PM (CET/CEST)

Meeting summary

Agenda

  1. Organizational matters and News
  2. Report from ELMI 2025
  3. Update on NBO-Q camera model & glossary
  4. Report from paper working group
  5. Next steps
Summary
The meeting opened with updates from SC and WG7 meetings, including a report from the NBO-Q camera model and glossary project.
Encouraging news was provided about Nature Publishing Group implementing reproducibility checklists inspired by QUAREP-LiMi’s work. These were mentioned in three recent editorials across major journals. However, concerns were raised as essential information is still missing.  A broader conversation on FAIR data sharing followed, highlighting the need to better recognize the cost and effort of data acquisition. QUAREP is encouraged to engage more actively in this direction.
Feedback from ELMI 2025 was very positive—QUAREP-led workshops were well attended and sparked interest among participants, many of whom were new to the initiative. This encouraged us to strengthen our outreach efforts for future international meetings, including next year’s ELMI.
Finally, the paper working group is drafting a publication outlining the foundation of the WG2 protocols. While initial writing has begun, broader input is needed. Future publishing plans for the automation tool and data samples  will depend on the setup of OMERO and collaboration with companies.
 

Meeting documentation

52nd meeting, 12th of May 2025

Meeting date

12/05/2025 @ 5:00 PM (CET/CEST)

Meeting summary

Agenda

  1. Organizational matters and News
  2. QUAREP-LiMi ELMI 2025 workshop contribution
  3. Report from OMERO subgroup meeting
  4. Update on NBO-Q camera model & glossary
  5. Report from paper working group
  6. Next steps

Summary

We started the meeting with discussing our summer meeting scenario. Due to a public holiday and ELMI 2025, we decided to shift our June meeting to June 23rd. In addition, we decided to skip the meetings in July and August to have time for finishing the camera model and glossary, work on the paper, and have time for vacation. We decided to start again with the regular meeting schedule on September 8th.
This summer meeting organisation was followed by a report from the May steering committee meeting. One great news for WG2 was that the SC endorsed the terminology “dexel” for the detector element versus “pixel” as picture element. Next, we briefly discussed the current status of our ELMI workshop preparation.
This was followed by a report from the QUAREP-LiMi OMERO subgroup meeting. A naming convention was introduced by that subgroup, which everybody needs to follow. We discussed how to implement our spreadsheet terms and how to best automate the upload to OMERO. The WG2 co-chairs will look over tags and naming structure for WG2.
This discussion was followed by an update from the NBO-Q camera model and glossary group. The stakeholder group finished working on the hardware part and will now continue with the settings. The plan is to be finished by the end of this summer.
The WG2 paper working group reported from their first meeting where they summarised paper-related content from our past meeting minutes.
We finalised the meeting with summarising the next steps: finalise the NBO-Q camera model and glossary, work on our paper and collect data for it, support WG7 in their work to calibration metadata, and generalise the automation of our WG2 protocols collection to have it eventually working on all microscopy platforms.

Meeting documentation

51st meeting, 14th of April 2025

Meeting date

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

Meeting summary

After discussing possible scenarios for our WG2 work during summer, we reported from the SC meeting on April 1st. This was followed by a detailed report from the Annual QUAREP-LiMi Meeting that took place April 10th. The ELMI contribution preparation team reported the submission of three workshop abstracts. Approval was expected to be highly likely (by now all our submitted workshops have been accepted). The NBO-Q camera glossary team could report that the hardware part is finished! Next, the settings part will be tackled, but is not expected to take that long. The rest of the meeting we spend on collecting topics for WG2 to work on in the future: automation for our WG2 protocols, paper to accompany our WG2 protocol collection, collect data for it, NBO-Q model update for point detectors, amongst others. For each of these topics we need to find people to take the lead and define respective time lines.

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. Report from the Annual QUAREP-LiMi meeting
  3. ELMI 2025 workshop contribution
  4. Update on NBO-Q camera model & glossary
  5. Next steps

Summary

This meeting was a bit of a house-keeping meeting. After the report from the March SC meeting we briefly discusses our planned contributions to the Annual QUAREP-LiMi meeting. This was followed by setting up a time line and preparation group for organising our contribution to ELMI2025. Next, we had a quick update on the current status of our NBO-Q camera model and glossary project. We closed the meeting with discussing the next projects we need to tackle. We will first focus on preparing our paper and organising collection of data. We will also have to revisit our long-term goals as next big projects.

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

Memberlist WG 2

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