In exciting news from QUAREP-LiMi, three new staff members have joined forces as core QUAREP staff, for the first time in its history, to accelerate the project in various capacities. They were welcomed into the community with a vibrant meet and greet on 2. July. 2026. If you are a member and missed this event, watch a recording on Nextcloud
Feel free to reach out to them for domain specific topics, or just to say hi!
We are very happy to welcome Arnica, Jakub, and Nataliia in our midst and look forward to great things to come for the project!
Caterina Strambio De CastilliaPresenter(s): Caterina Strambio-De-Castillia *1
*- the workshop was presented on behalf of QUAREP-LiMi WG7-Metadata.
1. Program in Molecular Medicine, UMass Chan Medical School
A major output of QUAREP-LiMi is the Light-Microscopy Metadata Model (LiMi-Model) [1, 2], developed by the QUAREP-LiMi Metadata Working Group (WG7) in collaboration with BioImaging North America, the 4D Nucleome consortium and OME. The LiMi-Model was designed to harmonize the description of light microscopy hardware, acquisition settings, and quality-control metrics in order to enhance image quality and reproducibility, and to fulfill the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.
Specifically, the LiMi-Model aims to: (1) promote the harmonized generation and pre-publication management of image datasets that are FAIR by design; (2) facilitate the deposition of FAIR microscopy datasets to public image data repositories; (3) facilitate data reuse and the extraction of quantitative information from image data using advanced bioimage analysis techniques, including AI/ML; and (4) define the light microscopy implementation of the Image Acquisition module of the Recommended Metadata for Biological Images (REMBI) guidelines [3].
The workshop will open with a general introduction to the purpose and scope of the LiMi-Model, situating it within the broader landscape of community initiatives. These include the recently published minimal reporting recommendations for light microscopy [4], REMBI, the International Standards Organization, imaging modality ontologies (such as FBbi and EDAM-bioimaging), and an emerging vision for next-generation metadata schema definition languages. This will be followed by a presentation of the LiMi-Model website [1] and interactive LiMi-Model Viewer, a tool designed to help community members navigate and understand the content of the model. The workshop will conclude with an overview of the LiMi-Model’s governance structure and an explanation of how community members can engage with and contribute to its ongoing development. As a concrete example of this process, the workshop will introduce the recent Camera Module revision, conducted in partnership with camera manufacturers whose outcomes will also be presented in a related poster presented in collaboration with QUAREP-WG2.
The formal presentations will be followed by an open discussion in which attendees are encouraged to provide feedback and help shape the future direction of the LiMi-Model.
[1] https://quarep.org/working-groups/wg-7-metadata/limi-model
[2] https://doi.org/10.1038/s41592-021-01327-9
[3] https://doi.org/10.1038/s41592-021-01166-8
[4] https://doi.org/10.1083/jcb.202601032
Hans Fried1, Roland Nitschke2, Kees van der Oord3, Maria M. Azevedo4,51. CRFS – Light Microscope Facility, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
2. Life Imaging Center and Signalling Research Centre CIBSS, University of Freiburg, Germany
3. Nikon Europe BV, Amstelveen, Netherlands
4. Advanced Light Microscopy Scientific Platform, i3S – Instituto de Investigação e Inovação em Saúde | Porto, Portugal
5. University of Porto
Accurate multi‑colour imaging requires that signals from the same physical location co‑localise across channels. Chromatic aberration is a major source of spatial error in multi‑colour fluorescence microscopy. Therefore, rigorous co‑registration is essential for reliable interpretation of spatial relationships in biological specimens.
In this workshop, we will briefly explain the key steps of preparing a bead sample for co-registration assessment, show the main considerations for image acquisition (1), and show you how to analyze the obtained images using Fiji/ImageJ (2). We will also demonstrate how specific objective‑related factors can influence co‑registration performance. Finally, we will share practical hints and tips to support routine co‑registration analysis.
(1) Dauphin A., Azevedo, M., et al. Protocols.io, Ensuring accurate co-registration measurement for quality control of Single Point Confocal Laser Scanning Microscopes – V1, dx.doi.org/10.17504/protocols.io.q26g7yrj8gwz/v1
(2) Faklaris, O. et al. Quality assessment in light microscopy for routine use through simple tools and robust metrics. J Cell Biol 221, doi:10.1083/jcb.202107093 (2022).
Glyn Nelson, Ioannis Alexopoulos, Yury Belyaev
The Point Spread Function (PSF), which describes the response of an optical system to a point source, is a key quality control of a microscope. Regular measurements, conducted with consistent tools, methods, and protocols, along with the calculation of robust metrics enable the monitoring of the microscope performance and therefore ensure better reproducibility of scientific experiments. During this workshop, we will show briefly how to prepare a bead slide, how to perform an acquisition, and finally how to analyze the PSF with open-source tools (1, 2). We will give some tips to troubleshooting PSFs that have an abnormal shape or are far from the theoretical expected size. We will also demonstrate the upload of the analysis results to OMERO, a database that will help monitor PSFs over time. We will use the protocols and metrics that are defined in the framework of the QUAREP-LiMi consortium’s WG5 (3).
1. Faklaris O., et al. “Quality Assessment in Light Microscopy for Routine Use through Simple Tools and Robust Metrics.” Journal of Cell Biology 221, no. 11 (2022): e202107093. https://doi.org/10.1083/jcb.202107093.
2. https://github.com/MontpellierRessourcesImagerie/MetroloJ_QC
3. Nelson G., et al. Protocolos.io, Monitoring the point spread function for quality control of confocal microscopes , dx.doi.org/10.17504/protocols.io.bp2l61ww1vqe/v1
Britta Schroth-Diez, Kees van der Oorda Nikon Europe B.V.
b Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Germany
The QUAREP-LiMi Tool Kit [1] was developed by the QUAREP-LiMi community to reduce the time needed to run periodic quality assessment protocols and organize the performance data acquired. During this workshop we will present its basic features and latest developments.
In accordance to the protocol defined by the QUAREP-LiMi WG 1 [2] the Tool Kit integrates user friendly interfaces for the assessment of illumination power and stability. These interfaces are already available for the Nikon and Zeiss acquistion software.
In addition, the Tool Kit includes support for the protocols for detector gain, dynamic range and noise assessment developed by the QUAREP-LiMi WG2 [2].
A highlight of the Tool Kit is its data browser. Thanks to the organized presentation of the performance metrics it is easier to diagnose problems – e.g. a small but steady power decrease over months– and take corrective and preventive actions before they become detrimental.
The Tool Kit functionality will be demonstrated during the workshop, where we will emphasize important details of the protocols.
[1] https://github.com/QUAREP-LiMi/QUAREP-LiMi-Tool-Kit
[2] https://www.protocols.io/workspaces/quarep-limi/publications
Britta Schroth-Diez, Kees van der Oord, Ruediger Bader1. Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden Germany
2. Nikon Europe BV
3. Hamamatsu Photonics Europe
QUAREP-LiMi Working Group 2 (WG2) developed a set of protocols [1] which focuses on the characterization and monitoring of the performance of light microscope detection systems, which collects light from the sample at the microscope and helps to convert the “arbitrary digital units” (ADU) provided by the microscope into “number of photons” detected.
The protocols collection is built around the photon transfer curve (PTC) method [2]. The goals of these protocols are to achieve 1) experiment quality control, 2) monitoring instrument quality over time, and 3) detailed detection system characterization. The protocols include both point and area detectors, allowing researchers to select appropriate methods based on their specific detection systems.
During the workshop, we will demonstrate how to use the protocols to acquire images and upload them in the software [3] to characterize the photon conversation factor (PCF photons/ADU), readnoise, background and dynamic range of a light microscopy detection system. The set includes protocols on sample preparation, data acquisition, and analysis. Furthermore, we will demonstrate its integration in the QUAREP-LiMi Tool Kit [4].
[1] Characterization of the Photon Conversion Factor, Noise, and Dynamic Range of Light Microscope Detection Systems – https://dx.doi.org/10.17504/protocols.io.14egn61pyl5d/v1
[2] Janesick JR. 2007. Photon Transfer. SPIE. https://dx.doi.org/10.1117/3.725073
[3] McFadden D. 2022. GUI Calibration Tool. https://github.com/bionanoimaging/NanoImagingPack/releases
[4] QUAREP-LiMi Tool Kit, https://github.com/QUAREP-LiMi/QUAREP-LiMi-Tool-Kit
QUAREP-LiMi WG3 was pleased to host a webinar presented by Daniel Schröder on the topic of the "Universal Laser Engine" with an improved homogeneous illumination profile.
The webinar introduced a versatile laser excitation platform designed for advanced fluorescence microscopy and highlighted its applications across multiple imaging modalities.
We are pleased to announce that the QUAREP-LiMi consortium will be presenting five specialized workshops at the upcoming European Light Microscopy Institute (ELMI) meeting. Our sessions are designed to provide researchers with frameworks for improving image quality, ensuring data reproducibility, and implementing rigorous quality control standards in microscopy. The workshops will cover five critical pillars of instrument characterization:
A new article, under the guidance of QUAREP-LiMi WG 11, on the minimal reporting requirements for light microscopy data has been published in the Journal of Cell Biology. You find the article here.
