QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopyMore about Open Access at the Crick
Authors listGlyn Nelson Ulrike Boehm Steve Bagley Peter Bajcsy Johanna Bischof Claire M Brown Aurélien Dauphin Ian M Dobbie John E Eriksson Orestis Faklaris Julia Fernandez‐Rodriguez Alexia Ferrand Laurent Gelman Ali Gheisari Hella Hartmann Christian Kukat Alex Laude Miso Mitkovski Sebastian Munck Alison J North Tobias M Rasse Ute Resch‐Genger Lucas C Schuetz Arne Seitz Caterina Strambio‐De‐Castillia Jason R Swedlow Ioannis Alexopoulos Karin Aumayr Sergiy Avilov Gert‐Jan Bakker Rodrigo R Bammann Andrea Bassi Hannes Beckert Sebastian Beer Yury Belyaev Jakob Bierwagen Konstantin A Birngruber Manel Bosch Juergen Breitlow Lisa A Cameron Joe Chalfoun James J Chambers Chieh‐Li Chen Eduardo Conde‐Sousa Alexander D Corbett Fabrice P Cordelieres Elaine Del Nery Ralf Dietzel Frank Eismann Elnaz Fazeli Andreas Felscher Hans Fried Nathalie Gaudreault Wah Ing Goh Thomas Guilbert Roland Hadleigh Peter Hemmerich Gerhard A Holst Michelle S Itano Claudia B Jaffe Helena K Jambor Stuart C Jarvis Antje Keppler David Kirchenbuechler Marcel Kirchner Norio Kobayashi Gabriel Krens Susanne Kunis Judith Lacoste Marco Marcello Gabriel G Martins Daniel J Metcalf Claire A Mitchell Joshua Moore Tobias Mueller Michael S Nelson Stephen Ogg Shuichi Onami Alexandra Palmer Perrine Paul‐Gilloteaux Jaime A Pimentel Laure Plantard Santosh Podder Elton Rexhepaj Arnaud Royon Markku A Saari Damien Schapman Vincent Schoonderwoert Britta Schroth‐Diez Stanley Schwartz Michael Shaw Martin Spitaler Martin T Stoeckl Damir Sudar Jeremie Teillon Stefan Terjung Roland Thuenauer Christian D Wilms Graham D Wright Roland Nitschke
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A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.