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Working Group 1     Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy The Consortium for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi), formed by the global community of practitioners, researchers, developers, service providers, funders, publishers, policy makers and industry related to the use of light microscopy, is committed to democratizing access to quantitative and reproducible light microscopy and the data generated by it. Our mission is to provide a comprehensive set

WG 1 – Illumination Power WG 2 – Detection system performance WG 3 – Uniformity of field – flatness WG 4 – System chromatic aberration and Co-registration WG 5 – Lateral and Axial Resolution WG 6 – Stage and Focus – precision and other WG 7 – Metadata WG 8 – Education, training and outreach WG 9 – Over all Planning + Funding WG 10 – Image Quality WG 11 – Microscopy publication standards WG 12 – Image Visualization and

WG 11 – Objectives WG11 will work together with scientific publishers to promote the adoption of best practices in the reporting of metadata (for both image acquisition and analysis) throughout scientific journals and books. Only by ensuring all relevant constituents researchers and imaging scientists submitting publications and designing research; editors, scientific publishers, and reviewers monitoring and preparing publications; and funders, researchers, and educators evaluating and disseminating publications) are working in concert can we raise the bar to ensure reproducibility in

Contact Information Life Imaging Center (LIC)Signalling Campus Freiburg (SCF)Habsburger Str. 4979104 Freiburg im BreisgauGermany The Life Imaging Center is part of the University of Freiburg. Albert-Ludwigs-Universität FreiburgFriedrichstraße 3979098 Freiburg im BreisgauGermany Contact Telefon: +49 761 203 – 0Fax: +49 761 203 – 4369info@uni-freiburg.dehttps://uni-freiburg.de General Liability The University of Freiburg is a corporation of public law represented legally by the rector Prof. Dr. Kerstin Krieglstein. Supervisory Authority Ministry for Science, Research and Arts of Baden-Württemberg Königstraße 4670173 StuttgartGermany Sales tax identification

Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy The Consortium for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy (QUAREP-LiMi), formed by the global community of practitioners, researchers, developers, service providers, funders, publishers, policy makers and industry related to the use of light microscopy, is committed to democratising access to quantitative and reproducible light microscopy and the data generated by it. Our mission is to provide a comprehensive set of community-agreed guidelines, protocols, automation

Network Communities Advanced Bioimaging Support (ABiS) Africa BioImaging Consortium (ABRC) Association of Biomolecular Resource Facilities – Light Microscopy (ABRF) BioImaging NorthAmerica (BINA) BioImagingUK Canada BioImaging (CBIBIC) European Light Microscopy Initiative (ELMI) Euro Bioimaging (EUROBIO) German BioImaging (GerBi) Global Bioimaging Microscopie Photonique de Fluorescence Multidimensionnelle (RTMFM) Netherlands Society for Microscopy (NVM) The Open Microscopy Environment (OME) Portugese Plattform of BioImaging (PPBI) Standardization Organizations European machine vision association (EMVA) Federal Institute for Material Research and Testing (BAM) German Institute for standardization (DIN)

Public Protocols All protocols are available on protocols.io Working Group 1 – Illumination Power 2025 27th of January Illumination Power, Stability and Linearity Measurements for Confocal, Widefield and Multiphoton Microscopes V.3 Authors: Nathalie Gaudreault1, Luis-Francisco Acevedo-Hueso2, Rizwan Ali3, Sergiy V Avilov4, Steve Bagley5, Rodrigo R Bammann6, Fabio Barachati7, Laszlo Barna8, Valeria Berno9, Cristina Bertocchi10, Veronika Boczonadi11, Ulrike Boehm12, Manel Bosch13, Craig Brideau14, Mariana T Carvalho15, Nabanita Chatterjee16, Pina Colarusso17, Richard Cole18, Nasser Darwish-Miranda19, Suat Dervish20, Ralf Dietzel21, Sam Duwé22, Frank

If you have a Tool you want to share with the global community, submit it here, and through our partnership with MicroscopyDB other imaging network communities partnering with this effort will also be able to share your Tool on their webpage. A list of all current MicroscopyDB partners that are contributing to and sharing this content can be found at https://microscopydb.io/who-we-are/#partners. ​This resource is powered by MicroscopyDB and is just one of a number of resources, including Events, Jobs, Training and Education Resources available for the community to search and share.

WG 10 – Objectives Good image quality (IQ) is essential for any subsequent image processing, analysis, and presentation steps. However, the notion of IQ is very broad and encompasses concepts that might differ between various microscope types. The aims of WG10 are 1) to define a set of basic IQ parameters (quantitative criteria, metadata, QC metrics) for light microscopy; 2) to weight the significance of the individual parameters for different experimental techniques and microscope types; and 3) to facilitate the

WG 9 – Objectives The purpose of WG9 was to coordinate and promote the activities of QUAREP-LiMi. After the Bylaws have been accepted in the 7th general meeting WG 9 was dissolved. This task is now the purpose of the steering committee.  Past Meetings Meeting documentation Meeting date Meeting documentation Meeting date Meeting documentation Meeting date Meeting documentation Meeting date Meeting documentation Meeting date Meeting documentation Meeting date Meeting documentation Meeting date Meeting documentation Meeting date Meeting documentation Meeting date

WG 8 – Objectives The aim of the QUAREP-LiMi consortium is to enhance the quality, reliability, and  reproducibility of light microscopy data across the life and material sciences. WG8 will focus on an important aspect of quality of light microscopy data: the quality of training. This will encompass both principles of microscopy training, and how to train others to adopt the protocols developed in the other QUAREP-LiMi working groups. Note that WG8, formerly known as the “White Paper” work group,

WG 7 – Objectives The Work Group 7 focuses on various aspects of Image Metadata (initially primarily Microscopy Metadata but also Sample and Analysis Metadata). These span from defining and continually revising the 4DN-BINA-OME (NBO) Microscopy Metadata model, to facilitating metadata capture through user-friendly tools, to integrating the captured metadata into cloud-ready storage containers such as the newly developed Open Microscopy Environment (OME) Next-Generation File Format (NGFF). To promote the uptake of metadata tools and models, educational material and outreach

WG 6 – Objectives The mission of WG6 is to ensure the performance and QC of stage platforms and sample holders and the optomechanical focus of the optical system as it relates to X, Y, Z movement, stability, reproducibility, and repeatability. The goals are defining the terms typically used to address QC, providing standardization of the measurements and testing protocols, and establishing performance benchmarking levels. Though initially applying these towards confocal light microscopy, the WG will endeavor to include details

WG 5 – Objectives This WG focuses on the microscope lateral and axial resolution, which is essential for reporting size measurements of near- resolution limit objects or distances between them. Resolution is highly related to the objective quality but depends strongly upon other parameters ranging from the sample preparation to the signal detection. The WG aims to define sample preparation, image acquisition, and data analysis protocols for testing resolution, first using sub-resolution fluorescent bead preparations and second employing alternative pattern-based

WG 4 – Objectives Chromatic aberration refers to possible artifacts caused by the wavelength dependency of an imaging system’s optical properties, with the result that two colors arising from the same physical location within the sample appear separated in the image.  Such artifacts result from the optical design of the system (e.g., well-corrected versus poorly corrected objective lenses), the manufacturing tolerances of the system components, and the alignment of the optical components. Co-registration accuracy more generally refers to the system’s

WG 3 – Objectives Illumination field uniformity is critical for quantitative imaging when comparing fluorescence intensities across a field-of-view (FOV) or a large tile of images capturing an entire sample. If the illumination is not constant over a large area, the fluorescence intensities will not represent the inherent fluorescence but rather the location within the image. Thus, WG3 aims at defining a set of universal protocols to assess the uniformity of illumination (i.e., “flatness” of field) over the FOV of

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

WG 1 – Objectives Comparison of fluorescence intensities between images requires measurements of the illumination power and stability of the excitation light source. WG1 aims at establishing a recommended protocol for measuring the stability of a light source during both short- and long-term image acquisition sessions using calibrated external power sensors. This initial aim will be extended later to measure the absolute flux of light through the illumination path and irradiance of the sample. The initial protocol will be designed

QUAREP Calender QUAREP General Meetings QUAREP-LiMi at Seminars/Meetings/Conferences Explore the various conferences where QUAREP-LiMi has been actively involved, contributing presentations and engaging with the scientific community. Here, you can find details about past and upcoming events featuring our members and their valuable insights into quality assessment, reproducibility, and standardization in light microscopy. Community Events Below is a non-exhaustive list of upcoming events for the imaging community! This resource is powered by MicroscopyDB. If you have an event to share, please

QUAREP-LiMi resources QUAREP-LiMi on social media Publications All publications related to QUAREP-LiMi. Protocols All protocols which have been published by QUAREP-LiMi. Tools Some useful tools. Links Some links to network communities and standardization organizations.

Organizational Structure and Immediate Goals Having established the general goals and founding principles of the group, members of QUAREP-LiMi agreed upon a set of essential topics to address and established the following organizational structure on July 9th, 2020: The group aims to achieve specific deliverables and established that work will be conducted by individual working groups, each led by two or more co-chairs. All interested parties are welcome to participate, either as observing members or as active participants within one

Members All Memberlist QUAREP Last name First Name Town Organisation Affiliation Lab Affiliation Country Time Zone Aaron Jesse Ashburn HHMI Janelia Research Campus Private lab US UTC-4 Acevedo Luis Overland Park thya Industry US UTC-6 Acher Olivier Palaiseau HORIBA France Industry FR UTC+1 Acton Richard Cambridge Human Developmental Biology Initiative Univ. GB UTC+-0 Ahmadpour Noushin Winnipeg University of Manitoba Univ. CA UTC-5 Akçınar Salim Can Izmir Ege University Univ. TR UTC+3 Alexopoulos Ioannis Giessen ILH/CIGL Multiscale Imaging Platform Univ. DE

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