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Home / The Light Microscopy Metadata Model (LiMi-Model): Enabling the Generation and Sharing of Reproducible, Community-Harmonized FAIR Bioimage Data (QUAREP-LiMi WG7-Matadata) ELMI Workshop

The Light Microscopy Metadata Model (LiMi-Model): Enabling the Generation and Sharing of Reproducible, Community-Harmonized FAIR Bioimage Data (QUAREP-LiMi WG7-Matadata) ELMI Workshop

Caterina Strambio De Castillia Presenter(s): Caterina Strambio-De-Castillia *1 *- the workshop will 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

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WG4 Workshop at ELMI 2026: “Assessing the co-registration accuracy of a microscope”

Hans Fried1, Roland Nitschke2, Kees van der Oord3, Maria M. Azevedo4,5 1. 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.

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WG5 Workshop at ELMI 2026: “Monitoring Microscope Performance Using PSF Measurements”

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,

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WG1, WG2 and WG6 Present Workshop on Automation of QUAREP-LiMi Protocols at ELMI 2026

  Britta Schroth-Diez, Kees van der Oord a 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

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At ELMI 2026, WG2 hosted the workshop “Estimation of the Photon Conversion Factor, Noise and Dynamic Range of Light Microscope Detection Systems”

  Britta Schroth-Diez, Kees van der Oord, Ruediger Bader 1. 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

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Developing efficient ways to communicate (e.g. a common language) allows data producers and consumers to work closely together and ‘crack tough nuts’, that would have been too hard for either to take on alone. The cartoon is ‘Common language’ by Henning Falk (doi:10.5281/zenodo.12751376), ©2024 NumFOCUS, where it was published under a CC BY 4.0 licence.

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Daniel Schröder Webinar (QUAREP-LiMi WG3): Universal Laser Engine with an Improved Homogeneous Illumination Profile

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. Abstract The Universal Laser Engine is a user-friendly laserbox designed to provide a versatile excitation for advanced fluorescence microscopy. In a single box, it holds up to 6 laser wavelengths operating in modes

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Join the QUAREP-LiMi Workshops at ELMI

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: The QUAREP-LiMi Tool Kit (WGs 1 & 2): Discover how to streamline periodic quality assessments. We will present the latest developments in

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LiMi-Model Viewer

Instructions This viewer provides an interactive interface for exploring the LiMi-Model — the Light Microscopy Model developed and maintained by QUAREP-LiMi to standardize microscopy metadata specifications. To navigate: click the center of any node to expand or collapse its sub-elements and attributes. Click the “i” icon on any node to view a detailed description of that element. Nodes shown with a light grey fill and colored border are attributes, describing the specific characteristics captured for each element. To search: type a term in the search box and click Search. All

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LiMi-Model for Imaging Scientists

The LiMi Model helps microscopy users & scientists standardize data quality and reproducibility Microscopy users and imaging scientists benefit from the LiMi Model’s clear, community-driven framework for recording the metadata that matters most—from sample preparation and imaging conditions to microscope hardware and acquisition settings. By integrating the LiMi-Model into your workflows, you ensure that your image data is not only reproducible and high quality but also compliant with FAIR principles, making it easier to share, publish, and reanalyse. The LiMi-Model

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LiMi-Model for Funders & Publishers

The LiMi Model empowers funders and journals to power scientific progress! Funding agencies and journal-publishers are key players, together with scientists to ensure scientific rigor and transparency, in line with FAIR data practices. The LiMi Model empowers member organizations in the scientific funding and publishing landscape to interact with the scientific community through standardized language and metadata standards for recording and publishing groundbreaking research. This leads to not only imaging data reproducibility and reuse, but also accelerates scientific progress, today

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LiMi-Model for Vendors

The LiMi-Model helps manufacturers and industry partners help the community Instrument manufacturers and industry partners can base new product developments on the extensive groundwork done by and within the LiMi Model community. By planning and creating products aligned with the LiMi Model framework and definitions, you can tap into and address the needs of an evolving scientific market, filling existing commercial gaps across a wide range of products- from electronic notebooks to microscopy hardware or software, image analysis tools, data storage solutions, quality control procedures, all

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LiMi-Model for Developers

Leveraging the LiMi Model in Software Development The LiMi-Model provides a structured, community-agreed metadata framework for light microscopy. By aligning software design and implementation with the LiMi-Model, developers can build widely applied software tools inherently compatible with data quality control, reproducibility, and interoperability. There is strong interest in the microscopy community for robust applications that integrate seamlessly with emerging standards like OME-Zarr and tools like Micro-Meta App, supporting accurate metadata recording, FAIR data practices and accelerating scientific discovery through automation.  The community consensus behind the

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LiMi-Model_AK

Become WG 7 Member Join our next meeting LiMi-Model The Light-Microscopy (LiMi) Model organises agreed-upon metadata vocabulary and definitions of light microscopy hardware, acquisition settings, and quality-control metrics into a modular, flexible structure.  This approach supports sustainable, broad adoption within the global microscopy community and ensures the data produced are FAIR – Findable, Accessible, Interoperable, and Reusable A section of the LiMi-Model Viewer showing the primary and secondary branches of metadata fields Purpose Promote and implement a globally consistent approach

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Microscopy data is more than the microscopic object. A complete description of the microscopy experiment certainly crosses into the macroscopic domain!
“Macroscopic Data”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping.

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ImagingData_Lifecycle

Industry partners of QUAREP including manufacturers can deliver high impact solutions towards fairification of the entire imaging data lifecycle. “Imaging Data Lifecycle”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping.

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“Data annotation matters”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping.

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DatasetsAnonymous

“Data annoation matters”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping

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“Data available on request”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping

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“Macroscopic data”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping

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“Multiple Clients”, NFDI4BIOIMAGE Consortium (2024): NFDI4BIOIMAGE data management illustrations by Henning Falk, Zenodo, https://doi.org/10.5281/zenodo.14186100, is used under a CC-BY 4.0 license. Modifications to this illustration include cropping.

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LiMi-Model Viewer

Instructions This viewer provides an interactive interface for exploring the LiMi-Model — the Light Microscopy Model developed and maintained by QUAREP-LiMi to standardize microscopy metadata specifications. To navigate: click the center of any node to expand or collapse its sub-elements and attributes. Click the “i” icon on any node to view a detailed description of that element. Nodes shown with a light grey fill and colored border are attributes, describing the specific characteristics captured for each element. To search: type a term in the search box and click Search. All

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Breaking News

More than 700 members have joined QUAREP-LiMi

QUAREP-LiMi has reached another milestone. By the end of 2025 more than 700 members have joined QUAREP-LiMi. When we launched this initiative, we never imagined the community would grow to include so many members from 46 different countries around the globe. A heartfelt thank‑you to all our members for your continued support and contributions.

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