QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy.
Antje Keppler, Tobias Mueller, Joshua Moore, Claire A Mitchell, Daniel J Metcalf, Gabriel G Martins, Marco Marcello, Judith Lacoste, Susanne Kunis, Gabriel Krens, Norio Kobayashi, Marcel Kirchner, David Kirchenbuechler, Michael S Nelson, Stuart C Jarvis, Helena K Jambor, Claudia B Jaffe, Michelle S Itano, Gerhard A Holst, Peter Hemmerich, Roland Hadleigh, Thomas Guilbert, Wah Ing Goh, Nathalie Gaudreault, Hans Fried, Vincent Schoonderwoert, Roland Nitschke, Graham D Wright, Christian D Wilms, Roland Thuenauer, Stefan Terjung, Jeremie Teillon, Damir Sudar, Martin T Stoeckl, Martin Spitaler, Michael Shaw, Stanley Schwartz, Britta Schroth-Diez, Andreas Felscher, Damien Schapman, Markku A Saari, Arnaud Royon, Elton Rexhepaj, Santosh Podder, Laure Plantard, Jaime A Pimentel, Perrine Paul-Gilloteaux, Alexandra L Palmer, Shuichi Onami, Stephen Ogg, Laurent Gelman, Caterina Strambio-De-Castillia, Arne Seitz, Lucas C Schuetz, Ute Resch-Genger, Tobias M Rasse, Alison J North, Sebastian Munck, Miso Mitkovski, Alex Laude, Christian Kukat, Hella Hartmann, Ali Gheisari, Jason R Swedlow, Alexia Ferrand, Julia Fernandez-Rodriguez, Orestis Faklaris, John E Eriksson, Ian M Dobbie, Aurélien Dauphin, Claire M Brown, Johanna Bischof, Peter Bajcsy, Steve Bagley, Ulrike Boehm, Manel Bosch, Elnaz Fazeli, Frank Eismann, Ralf Dietzel, Elaine Del Nery, Fabrice P Cordelieres, Alexander D Corbett, Eduardo Conde-Sousa, Chieh-Li Chen, James J Chambers, Joe Chalfoun, Lisa A Cameron, Juergen Breitlow, Glyn Nelson, Konstantin A Birngruber, Jakob Bierwagen, Yury Belyaev, Sebastian Beer, Hannes Beckert, Andrea Bassi, Rodrigo R Bammann, Gert-Jan Bakker, Sergiy Avilov, Karin Aumayr, Ioannis Alexopoulos
Journal: Journal of microscopy
2021;284(1):56-73
PMID: 34214188
Abstract
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.
© 2021 The Authors. Journal of Microscopy published by JohnWiley & Sons Ltd on behalf of Royal Microscopical Society.
Address:
Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK.; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.; Visualisation, Irradiation & Analysis, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield, UK.; National Institute of Standards and Technology, Gaithersburg, Maryland, USA.; Euro-BioImaging, Heidelberg, Germany.; Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada.; Unité Génétique et Biologie du Développement U934, PICT-IBiSA, Institut Curie/Inserm/CNRS/PSL Research University, Paris, France.; Department of Biochemistry, University of Oxford, Oxford, Oxon, UK.; Turku Bioscience Centre, Euro-Bioimaging ERIC, Turku, Finland.; Biocampus, CNRS UAR 3426, Montpellier, France.; Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.; Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland.; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.; Light Microscopy Facility, CMCB Technology Platform, TU Dresden, Dresden, Germany.; FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany.; Light Microscopy Facility, Max Planck Institute of Experimental Medicine, Goettingen, Germany.; VIB BioImaging Core & VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department for Neuroscience, Leuven, Flanders, Belgium.; The Rockefeller University, New York, New York, USA.; Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.; Division Biophotonics, Federal Institute for Materials Research and Testing, Berlin, Germany.; European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany.; Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Vaud, Switzerland.; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.; Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.; General Instrumentation - Light Microscopy Facility, Faculty of Science, Radboud University, Nijmegen, The Netherlands.; BioOptics Facility, IMP - Research Institute of Molecular Pathology, Vienna, Austria.; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.; Department of Cell Biology (route 283), Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.; Scientifica Ltd., Uckfield, East Sussex, UK.; Dipartimento di Fisica, Politecnico di Milano, Milan, Italy.; Microscopy Core Facility, Medizinische Fakultät, Universität Bonn, Bonn, Germany.; Hamamatsu Photonics GmbH, Herrsching, Germany.; Microscopy Imaging Center, University of Bern, Bern, Switzerland.; AHF analysentechnik AG, Tuebingen, Germany.; TOPTICA Photonics AG, Graefelfing, Germany.; Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.; PicoQuant, Berlin, Germany.; Light Microscopy Core Facility, Department of Biology, Duke University, Durham, North Carolina, USA.; Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA.; Pathware, Seattle, Washington, USA.; i3S - Instituto de InvestigaÇão e InovaÇão em Saúde, Universidade do Porto, Porto, Portugal.; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.; Department of Physics and Astronomy, University of Exeter, Exeter, UK.; Bordeaux Imaging Center, Bordeaux, Nouvelle Aquitaine, France.; BioPhenics High-Content Screening Laboratory (PICT-IBiSA), Translational Research Department, Institut Curie - PSL Research University, Paris, France.; Omicron-Laserage Laserprodukte GmbH, Rodgau, Germany.; Carl Zeiss Microscopy GmbH, Jena, Germany.; University of Turku, Turku, Finland.; Coherent LaserSystems GmbH & Co. KG, Luebeck, Germany.; Light Microscope Facility, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.; Allen Institute for Cell Science, Seattle, Washington, USA.; A*STAR Microscopy Platform, Research Support Centre, Agency for Science, Technology and Research, Singapore, Singapore.; Institut Cochin, INSERM (U1016), CNRS (UMR 8104), Université de Paris (UMR-S1016), Paris, France.; Core Facility Imaging, Leibniz Institute on Aging, Jena, Germany.; Research & Science, PCO AG, Kelheim, Germany.; Neuroscience Microscopy Core, University of North Carolina, Chapel Hill, North Carolina, USA.; Lumencor, Inc., Beaverton, Oregon, USA.; Mildred-Scheel Nachwuchszentrum, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany.; Prior Scientific Instruments Limited, Cambridge, Cambridgeshire, UK.; EMBL Heidelberg, Global BioImaging, Heidelberg, Germany.; Northwestern University, Chicago, Illinois, USA.; RIKEN, Wako, Saitama, Japan.; Bioimaging Facility, Institute of Science and Technology Austria, Klosterneuburg, Austria.; University Osnabrueck, Biology/Chemistry, Osnabrueck, Germany.; MIA Cellavie Inc., Montreal, Quebec, Canada.; Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, Merseyside, UK.; Instituto Gulbenkian de Ciencia & Faculdade de Ciencias, University of Lisboa, Oeiras, Portugal.; Warwick Medical School, University of Warwick, Coventry, West Midlands, UK.; Gregor Mendel Institute of Molecular Plant Biology (GMI), Vienna, Austria.; City of Hope, Duarte, California, USA.; Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta, Canada.; RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan.; Advanced Light Microscopy, The Francis Crick Institute, London, UK.; Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, F-44000 Nantes, France.; Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.; Microscopy Facility, Department of Biology, Indian Institute of Science Education and Research Pune, Pune, India.; Sanofi Aventis, Chilly-Mazarin, Essone, France.; Argolight, Pessac, France.; Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.; UNIROUEN, INSERM, PRIMACEN, Normandie University, Rouen, France.; Scientific Volume Imaging bv, Hilversum, Noord-Holland, 1213VB, The Netherlands.; Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.; Nikon Instruments Inc. ISO Consultant, Melville, New York, USA.; National Physical Laboratory, Teddington, Middlesex, UK.; Imaging Facility, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany.; Bioimaging Center, University of Konstanz, Konstanz, Germany.; Quantitative Imaging Systems, Portland, Oregon, USA.; Bordeaux Imaging Center, Université de Bordeaux, Bordeaux, Gironde, France.; Technology Platform Microscopy and Image Analysis, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.; Life Imaging Center and BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
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