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
Valeria Berno
Imaging Facility Specialist at The Advanced Light and Electron Microscopy BioImaging Center (ALEMBIC) of San Raffaele Hospital
Co-Chair of WG 2
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
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: 8th December 2025, 5:00 pm
Upcoming meeting: 10th November 2025, 5:00 pm
Upcoming meeting: 13th October 2025, 5:00 pm
Last meeting: 8th September 2025, 5:00 pm
Release of protocols collection:
Separate protocols:
2. Sample Preparation – An Easy-to-Prepare Sample Slide
- 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
- 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
- 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
54th meeting, 8th of September 2025
Meeting date
08/09/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- Update on NBO-Q camera model & glossary
- Updates after the summer break (paper, automation…)
- Decide on next priorities
The meeting welcomed new member Kemp Watson and covered organizational updates from the steering committee, including various project developments and upcoming meetings scheduled for October and November. The working group discussed their focus on detection system performance, including camera models and standardized terminology for microscopy systems, while also addressing the progress of a manuscript related to protocol series. The team reviewed developments of the Nikon toolkit and discussed next steps for their project, including the sequential completion of camera work before moving to other detector types.
53rd meeting, 23rd of June 2025
Meeting date
23/06/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- Report from ELMI 2025
- Update on NBO-Q camera model & glossary
- Report from paper working group
- Next steps
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.
52nd meeting, 12th of May 2025
Meeting date
12/05/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda
- Organizational matters and News
- QUAREP-LiMi ELMI 2025 workshop contribution
- Report from OMERO subgroup meeting
- Update on NBO-Q camera model & glossary
- Report from paper working group
- 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.
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.
50th meeting, 10th of March 2025
Meeting date
10/03/2025 @ 5:00 PM (CET/CEST)
Meeting summary
Agenda points
- Organizational matters and News
- Report from the Annual QUAREP-LiMi meeting
- ELMI 2025 workshop contribution
- Update on NBO-Q camera model & glossary
- 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.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.
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
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
Memberlist WG 2
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