scispace - formally typeset
Search or ask a question
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.

Papers
More filters
Journal ArticleDOI
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

Journal ArticleDOI
Glyn Nelson1, Ulrike Boehm2, Steve Bagley, Peter Bajcsy3, Johanna Bischof, Claire M. Brown4, Aurelien Dauphin5, Ian M. Dobbie6, John E Eriksson, Orestis Faklaris7, Julia Fernandez-Rodriguez8, Alexia Ferrand9, Laurent Gelman10, Ali Gheisari11, Hella Hartmann11, Christian Kukat12, Alex Laude1, Miso Mitkovski12, Sebastian Munck13, Alison J. North14, Tobias M. Rasse12, Ute Resch-Genger15, Lucas C Schuetz, Arne Seitz16, Caterina Strambio-De-Castillia17, Jason R. Swedlow18, Ioannis Alexopoulos19, Karin Aumayr20, Sergiy V. Avilov12, Gert-Jan Bakker, Rodrigo R Bammann21, Andrea Bassi22, Hannes Beckert23, Sebastian Beer24, Yury Belyaev25, Jakob Bierwagen, Konstantin A Birngruber, Manel Bosch26, Juergen Breitlow, Lisa A. Cameron27, Joe Chalfoun3, James J. Chambers28, Chieh-Li Chen, Eduardo Conde-Sousa29, Alexander D. Corbett30, Fabrice P. Cordelières, Elaine Del Nery5, Ralf Dietzel, Frank Eismann31, Elnaz Fazeli32, Andreas Felscher, Hans-Ulrich Fried33, Nathalie Gaudreault34, Wah Ing Goh35, Thomas Guilbert36, Roland Hadleigh21, Peter Hemmerich37, Gerhard A Holst, Michelle S. Itano38, Claudia B Jaffe, Helena Jambor11, Stuart C Jarvis, Antje Keppler39, David Kirchenbuechler40, Marcel Kirchner12, Norio Kobayashi, Gabriel Krens41, Susanne Kunis, Judith Lacoste, Marco Marcello42, Gabriel G. Martins43, Daniel J Metcalf21, Claire A. Mitchell44, Joshua Moore18, Tobias Mueller45, Michael S. Nelson46, Stephen Ogg47, Shuichi Onami, Alexandra L Palmer48, Perrine Paul-Gilloteaux49, Jaime A. Pimentel50, Laure Plantard10, Santosh Podder51, Elton Rexhepaj, Arnaud Royon, Markku Saari32, Damien Schapman52, Vincent Schoonderwoert, Britta Schroth-Diez12, Stanley Schwartz, Michael Shaw53, Martin Spitaler12, Martin T Stoeckl54, Damir Sudar, Jeremie Teillon55, Stefan Terjung, Roland Thuenauer56, Christian D Wilms21, Graham D. Wright35, Roland Nitschke57 
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

Journal ArticleDOI
Glyn Nelson1, Ulrike Boehm2, Steve Bagley, Peter Bajcsy3, Johanna Bischof, Claire M. Brown4, Aurelien Dauphin5, Ian M. Dobbie6, John E Eriksson, Orestis Faklaris7, Julia Fernandez-Rodriguez8, Alexia Ferrand9, Laurent Gelman10, Ali Gheisari11, Hella Hartmann11, Christian Kukat12, Alex Laude1, Miso Mitkovski12, Sebastian Munck13, Alison J. North14, Tobias M. Rasse12, Ute Resch-Genger15, Lucas C Schuetz, Arne Seitz16, Caterina Strambio-De-Castillia17, Jason R. Swedlow18, Ioannis Alexopoulos19, Karin Aumayr20, Sergiy V. Avilov12, Gert-Jan Bakker, Rodrigo R Bammann21, Andrea Bassi22, Hannes Beckert23, Sebastian Beer24, Yury Belyaev25, Jakob Bierwagen, Konstantin A Birngruber, Manel Bosch26, Juergen Breitlow, Lisa A. Cameron27, Joe Chalfoun3, James J. Chambers28, Chieh-Li Chen, Eduardo Conde-Sousa29, Alexander D. Corbett30, Fabrice P. Cordelières, Elaine Del Nery5, Ralf Dietzel, Frank Eismann31, Elnaz Fazeli32, Andreas Felscher, Hans-Ulrich Fried33, Nathalie Gaudreault34, Wah Ing Goh35, Thomas Guilbert36, Roland Hadleigh21, Peter Hemmerich37, Gerhard A Holst, Michelle S. Itano38, Claudia B Jaffe, Helena Jambor11, Stuart C Jarvis, Antje Keppler39, David Kirchenbuechler40, Marcel Kirchner12, Norio Kobayashi, Gabriel Krens41, Susanne Kunis, Judith Lacoste, Marco Marcello42, Gabriel G. Martins43, Daniel J Metcalf21, Claire A. Mitchell44, Joshua Moore18, Tobias Mueller45, Michael S. Nelson46, Stephen Ogg47, Shuichi Onami, Alexandra L Palmer48, Perrine Paul-Gilloteaux49, Jaime A. Pimentel50, Laure Plantard10, Santosh Podder51, Elton Rexhepaj, Arnaud Royon, Markku Saari32, Damien Schapman52, Vincent Schoonderwoert, Britta Schroth-Diez12, Stanley Schwartz, Michael Shaw53, Martin Spitaler12, Martin T Stoeckl54, Damir Sudar, Jeremie Teillon55, Stefan Terjung, Roland Thuenauer56, Christian D Wilms21, Graham D. Wright35, Roland Nitschke57 
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


Cited by
More filters
Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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

Posted Content
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