Author
Steve Bagley
Bio: Steve Bagley is an academic researcher. The author has contributed to research in topics: Quality assurance & Quality control. The author has an hindex of 3, co-authored 3 publications receiving 21 citations.
Topics: Quality assurance, Quality control
Papers
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Howard Hughes Medical Institute1, Newcastle University2, McGill University3, National Institute of Standards and Technology4, PSL Research University5, University of Oxford6, University of Montpellier7, University of Gothenburg8, University of Basel9, Friedrich Miescher Institute for Biomedical Research10, Dresden University of Technology11, Max Planck Society12, Katholieke Universiteit Leuven13, Rockefeller University14, Bundesanstalt für Materialforschung und -prüfung15, École Polytechnique Fédérale de Lausanne16, University of Massachusetts Medical School17, University of Dundee18, University of Freiburg19
TL;DR: The QUAREP-LiMi project as mentioned in this paper aims to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images through a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.
Abstract: The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.
31 citations
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Newcastle University1, Howard Hughes Medical Institute2, National Institute of Standards and Technology3, McGill University4, PSL Research University5, University of Oxford6, Centre national de la recherche scientifique7, University of Gothenburg8, University of Basel9, Friedrich Miescher Institute for Biomedical Research10, Dresden University of Technology11, Max Planck Society12, Katholieke Universiteit Leuven13, Rockefeller University14, Bundesanstalt für Materialforschung und -prüfung15, École Polytechnique Fédérale de Lausanne16, University of Massachusetts Medical School17, University of Dundee18, Radboud University Nijmegen19, Research Institute of Molecular Pathology20, East Sussex County Council21, Polytechnic University of Milan22, University of Bonn23, Hamamatsu Photonics24, University of Bern25, University of Barcelona26, Duke University27, University of Massachusetts Amherst28, University of Porto29, University of Exeter30, Carl Zeiss AG31, University of Turku32, German Center for Neurodegenerative Diseases33, Allen Institute for Cell Science34, Agency for Science, Technology and Research35, University of Paris36, National Institutes of Health37, University of North Carolina at Chapel Hill38, European Bioinformatics Institute39, Northwestern University40, Institute of Science and Technology Austria41, University of Liverpool42, Instituto Gulbenkian de Ciência43, University of Warwick44, Gregor Mendel Institute45, City of Hope National Medical Center46, University of Alberta47, Francis Crick Institute48, University of Nantes49, National Autonomous University of Mexico50, Indian Institute of Science Education and Research, Pune51, French Institute of Health and Medical Research52, National Physical Laboratory53, University of Konstanz54, University of Bordeaux55, Heinrich Pette Institute56, University of Freiburg57
TL;DR: The QUAREP-LiMi initiative as mentioned in this paper aims to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
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 experiments1 . 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 technique2,3 . 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. ENCODE4 ), 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 reproducibility5 . In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative6 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 models7,8 , and tools9,10 , 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 scientists11 , 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.
27 citations
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Newcastle University1, Howard Hughes Medical Institute2, National Institute of Standards and Technology3, McGill University4, PSL Research University5, University of Oxford6, Centre national de la recherche scientifique7, University of Gothenburg8, University of Basel9, Friedrich Miescher Institute for Biomedical Research10, Dresden University of Technology11, Max Planck Society12, Katholieke Universiteit Leuven13, Rockefeller University14, Bundesanstalt für Materialforschung und -prüfung15, École Polytechnique Fédérale de Lausanne16, University of Massachusetts Medical School17, University of Dundee18, Radboud University Nijmegen19, Research Institute of Molecular Pathology20, East Sussex County Council21, Polytechnic University of Milan22, University of Bonn23, Hamamatsu Photonics24, University of Bern25, University of Barcelona26, Duke University27, University of Massachusetts Amherst28, University of Porto29, University of Exeter30, Carl Zeiss AG31, University of Turku32, German Center for Neurodegenerative Diseases33, Allen Institute for Cell Science34, Agency for Science, Technology and Research35, University of Paris36, National Institutes of Health37, University of North Carolina at Chapel Hill38, European Bioinformatics Institute39, Northwestern University40, Institute of Science and Technology Austria41, University of Liverpool42, Instituto Gulbenkian de Ciência43, University of Warwick44, Gregor Mendel Institute45, City of Hope National Medical Center46, University of Alberta47, Francis Crick Institute48, University of Nantes49, National Autonomous University of Mexico50, Indian Institute of Science Education and Research, Pune51, French Institute of Health and Medical Research52, National Physical Laboratory53, University of Konstanz54, University of Bordeaux55, Heinrich Pette Institute56, University of Freiburg57
Abstract: 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.
8 citations
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TL;DR: The authors provide guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities with the goal of improving microscopy reporting, rigor and reproducibility.
Abstract: Although fluorescence microscopy is ubiquitous in biomedical research, microscopy methods reporting is inconsistent and perhaps undervalued. We emphasize the importance of appropriate microscopy methods reporting and seek to educate researchers about how microscopy metadata impact data interpretation. We provide comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities. We aim to improve microscopy reporting, thus improving the quality, rigor and reproducibility of image-based science. Comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities are reported with the goal of improving microscopy reporting, rigor and reproducibility.
47 citations
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European Bioinformatics Institute1, SLAC National Accelerator Laboratory2, Francis Crick Institute3, University of Massachusetts Medical School4, Instituto Gulbenkian de Ciência5, National Institutes of Health6, Birkbeck, University of London7, University of Dundee8, University of Bristol9, Wellcome Trust Sanger Institute10, Katholieke Universiteit Leuven11, Carl Zeiss AG12, University of Nantes13, Johnson & Johnson14, Åbo Akademi University15, European Molecular Biology Organization16, GlaxoSmithKline17, King's College London18, National Physical Laboratory19, University of Konstanz20, Leiden University Medical Center21, Wellcome Trust Centre for Human Genetics22
TL;DR: In this paper, the authors propose metadata guidelines to address the needs of diverse communities within light and electron microscopy within microscopy, and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.
Abstract: Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.
39 citations
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University of Dundee1, Åbo Akademi University2, European Bioinformatics Institute3, Monash University4, University of Queensland5, University of the Republic6, University of Sydney7, University of Chile8, McGill University9, National Autonomous University of Mexico10, Stellenbosch University11, University of Turin12, National Research Council13
TL;DR: In this article, the authors present criteria for globally applicable guidelines for open image data tools and resources for the rapidly developing fields of biological and biomedical imaging, which are used throughout the life and biomedical sciences to understand mechanisms in biology and diagnosis and therapy in animal and human medicine.
Abstract: Imaging technologies are used throughout the life and biomedical sciences to understand mechanisms in biology and diagnosis and therapy in animal and human medicine. We present criteria for globally applicable guidelines for open image data tools and resources for the rapidly developing fields of biological and biomedical imaging.
36 citations
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TL;DR: The Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard as discussed by the authors is based on best practices from genomics and microscopy of cultured cells and model organisms.
Abstract: The imminent release of atlases combining highly multiplexed tissue imaging with single cell sequencing and other omics data from human tissues and tumors creates an urgent need for data and metadata standards compliant with emerging and traditional approaches to histology. We describe the development of a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that draws on best practices from genomics and microscopy of cultured cells and model organisms.
23 citations