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

We welcome our first member from the United Arab Emirates. Rachid Rezgui of NYU Abu Dhabi joined the Working Groups 1-7, 9, 10 and 13. Change the Quality of Light Microscopy Imaging as member of QUAREP-LiMi join us here.

The WG 1 released its first protocol “Illumination Power and Illumination Stability“. The protocol is featured on

Beside step-by-step instructions, the protocol provides:

We welcome our first member from the Ecuador. William Narvaez joined the Working Groups 1, 3, 5, 9 and 11. Change the Quality of Light Microscopy Imaging as member of QUAREP-LiMi join us here.

 

Upcoming meeting: 8th September 2025, 5:00 pm
Upcoming meeting: 23rd June 2025, 5:00 pm
Last meeting: 12th May 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.  

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

41st meeting, 13th of May 2024

Meeting date

13/05/2024 @ 5:00 PM (CET/CEST)

Meeting summary

During the organisational and news part, the respective participants reported from the general assembly meeting which took place online on April 16th 2024. Subsequently, the steering committee (SC) was formed and held its inauguration meeting, which our SC members reported from as well. The main topic of our 41st meeting was to discuss and finalise our WG2 workshop on camera topics at ELMI2024. The workshop scheduled was presented, discussed, and approved. A new development was the joining of WG13 in our workshop withe the topic of avoidance of illumination overhead. In addition, we talked about the next steps to finalise and publish our protocols. A meeting with Emma Ganley from protools.io was planned for the next day. We will report from this meeting in the June meeting. As an additional topic, Gert-Jan introduced a possible new standardised light source which could be cheap and easy to built.

Meeting documentation

40th meeting, 8th of April 2024

Meeting date

08/04/2024 @ 5:00 PM (CET/CEST)

Meeting summary

After the organisational and news part, we started the meeting with the election of our SC representative, Britta Schroth-Diez, by acclamation. The main topic of our 40th meeting was to discuss our potential contribution to the ELMI2024 community space. As a prerequisite we talked about the needed steps to finalise and ideally publish our protocols until ELMI2024 in June or July. One option is to have a preliminary version and check it during ELMI. We have to ensure to keep the protocols simple with trouble-shooting tips and tricks, also including instructive videos. We will work in smaller groups on the protocols until the May meeting. For our WG2 contribution to the ELMI2024 community space, we are going to do a similar scenario as done last year. Focus will be on ongoing work to automate the workflow. We will also mention our work on the camera glossary. The presenters will meet to prepare a workshop schedule to be shown and discussed during our May meeting.

Meeting documentation

39th meeting, 11th of March 2024

Meeting date

11/05/2024 @ 5:00 PM (CET/CEST)

Meeting summary

Part of the meeting was planned to be the announcement of the results for our election of our WG2 co-chairs and representatives to the new governing bodies of QUAREP-LiMi (ERB, OB, SC). Unfortunately, we had some difficulties with the online voting platform. Therefore, we decided to do the elections via acclamation during the meeting. Results of the elections are: Co-chairs (for the next 2 years term): Gert-Jan Bakker, Valeria Berno, David McFadden, and Britta Schroth-Diez. ERB representative: David Grunwald, OB representative: Gerhard Holst. SC representative election will take place in our April meeting. The main topic of our 39th meeting was to discuss our potential contribution to the ELMI2024 community space. We agreed to do a similar workshop as we did last year, with particularly focusing on automation of the workflow and presentation of our protocols. To be able to do so, we need to finalise and ideally publish our protocols until ELMI2024 in June. To be able to do so, we formed two smaller groups to go over the protocols again until the April meeting. In addition to our protocols efforts, we aim to also finalise the joined WG2-7camera glossary project and keep working on our first paper.

Meeting documentation

38th meeting, 12th of February 2024

Meeting date

12/02/2024 @ 5:00 PM (CET/CEST)

Meeting summary

The main topic of the meeting was the presentation of the by-law initiative by David Grundwald. You can find the current versions of the by-law documents and the slide deck of the by-law presentation in our 38th meeting folder. The by-laws and their approval will also be the main topic of our QUAREP-LiMi general assembly meeting on April 16th 2024.
In addition to this important topic we also discussed our potential contribution to the community space during ELMI 2024. We agreed to discuss this in more detail during our March meeting.
Gert-Jan gave a literature pitch about a very interesting Mulit-photon microsocpy QC paper published recently in bioRxiv. His presentation can be found in our 38th meeting folder as well,
In addition, it was reported that the first version of the camera model and glossary is finished. It will be revisited and discussed by the camera model revision stakeholder group before it will be presented as a suggestion for model change to the whole QUAREP-LiMi consortium. The meeting finished with a short summary and reminder about the work to be done towards our paper.

Meeting documentation

37th meeting, 11th of December 2023

Meeting date

11/12/2023 @ 5:00 PM (CET/CEST)

Meeting summary

In short, the main topic of this meeting was to discuss a potential collaboration with the MetrologyJ_QC group. For that, Orestis and Julien joined us as guests.

We found that both our efforts are complementary and thus can nicely be combined. The MetrologyJ_QC analysis tool focusses on calculating camera read noise, DSNU (dark signal non-uniformity), and hot and cold pixels. Our WG2 analysis tool focusses on calculating the photon-conversion factor. In addition, we as WG2 aim to combine our analysis with an easy to use (automated) acquisition protocol.

Generally, QUAREP-LiMi needs to develop a nice overarching framework for running all our quality control scripts automatically together easily in one tool. Someone needs to take the lead for this endeavour. There is already great groundwork being done, thanks to Kees, for WG1 and also for WG2.

In addition to this main topic there was the report from the last WG9 and WG7 meetings as well as a short review of the next steps to be done toward our paper.

Meeting documentation

36th meeting, 13th of November 2023

Meeting date

13/11/2023 @ 5:00 PM (CET/CEST)

Meeting summary

After a short session of QUAREP-LiMi news and updates on our other running projects, we mainly focussed on our planned paper which should accompany the publishing of our protocols. We discussed main aspects, determined topics which need to be addressed and members who our responsible for working on the topics. To be able to have time to do so, we decide to skip the meeting in January 2024.

Meeting documentation

35th meeting, 10th of October 2023

Meeting date

10/10/2023 @ 5:00 AM (CET/CEST)

Meeting documentation

Memberlist WG 2

Last nameFirst NameTownOrganisation AffiliationLab AffiliationCountryTime Zone
Acevedo Luis Overland Park thya Industry US UTC-6
Alshafie Walaa Ashburn Janelia research campus Univ. US UTC-4
Avilov Sergiy Freiburg Max Planck Institute of Immunobiology and Epigenetics MPG DE UTC+2
Bakker Gert-Jan Nijmegen NVvM Univ. NL UTC+2
Bammann Rodrigo Uckfield Scientifica Industry GB UTC+1
Banerjee Priyam New York Rockefeller University Univ. US UTC-5
Barna Laszlo Bloomington Indiana University Bloomington Gov. HU UTC+1
Beer Sebastian Hersching Hamamatsu Industry DE UTC+2
Bennett Sarah Coventry University of Warwick Univ. GB UTC+1
Bergles Eric San Jose Pavilion Integration Corporation Industry US UTC-8
Berno Valeria Milano Ospedale San Raffaele- ALEMBIC Gov. IT UTC+2
Bierwagen Jakob Tuebingen AHF Industry DE UTC+2
Boczonadi Veronika Newcastle Newcastle University Univ. GB UTC+-0
Bosch Manel Barcelona University of Barcelona CCITUB Univ. ES UTC+2
Cadby Ashley Sheffield University of Sheffield Univ. GB UTC+-0
Cappellaro Markus München Carl Zeiss Microscopy Industry DE UTC+1
Carvalho Mariana Braga INL – International Iberian Nanotechnology Laboratory EU-Org PT UTC+-0
Catrina Irina New York Yeshiva University Univ. US UTC-5
Ceccarelli Raino Rome CrestOptics S.p.A. Industry IT UTC+1
Cesbron Yann Klosterneuburg Institute of Science and Technology Austria Gov. AT UTC+1
Chacko Jenu Madison University of Wisconsin-Madison Univ. US UTC-6
Chen Lily Hayward Eikon Therapeutics Industry US UTC-8
Chiritescu Catalin Champaign Phi Optics, Inc. Industry US UTC-6
Christensen Nynne Copenhagen University of Copenhagen, Center for Advanced Bioimaging Univ. DK UTC+1
Clements Darran Cambridge University of Cambridge Univ. GB UTC+1
Cole Louise Sydney University of Technology Univ. AU UTC+11
Cortes Luisa Coimbra Center for Neuroscience and Cell Biology Univ. PT UTC+0
Dencevski Aleksa Belgrade Institute of physics Belgrade Univ. CS UTC+1
Dervish Suat Westmead Westmead Institute for Medical Research Gov. AU UTC+10
Diez-Guerra F. Javier Madrid CBMSO (CSIC-UAM) Univ. ES UTC+2
Doherty Glen New York Icahn School of Medicine at Mount Sinai Univ. US UTC-4
Drent Peter Amsterdam ONI Industry NL UTC+1
Duong Cao Nguyen Saarbrücken Leibniz Institute for New Materials Leibniz DE UTC+1
Egron Audrey Pessac Argolight Industry FR UTC+1
Eismann Frank Jena Carl Zeiss Microscopy GmbH Industry DE UTC+2
Eseola Alice Norwich The Sainsbury Laboratory Univ. GB UTC+1
Esner Milan Brno Ceitec Masaryk University Univ. CZ UTC+1
Faklaris Orestis Montpellier RTmfm Univ. FR UTC+2
Fu Yangting Bonn Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE) Helmholtz DE UTC+1
Fujimori Toshihiko Okazaki JP BioImaging Gov. JP UTC+9
Garcia Gonzalez Esther Didcot STFC, UKRI Gov. GB UTC+1
Gaudreault Nathalie Seattle Allen Institute Private lab US UTC-7
Gauthier Pascal Jonquiere RioTinto Private lab CA UTC+5
Gharagozlou Shadi Klosterneuburg Institute of science and technology Austria Univ. AT UTC+1
Giles Patrick Uckfield Scientifica Industry GB UTC+-0
Girard Philippe Paris Institut Jacques Monod – Université de Paris Univ. FR UTC+1
Graaff Anko Utrecht Hubrecht Institute Univ. NL UTC+1
Grunwald David Worcester University of Massachusetts Univ. US UTC-4
Gunkel Manuel Heidelberg EMBL Heidelberg EU-Org DE UTC+2
Halter Michael Gaithersburg NIST Gov. US UTC-4
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