A1 Refereed original research article in a scientific journal
QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
Authors: Nelson Glyn, Boehm Ulrike, Bagley Steve, Bajcsy Peter, Bischof Johanna, Brown Claire M., Dauphin Aurélien, Dobbie Ian M., Eriksson John E., Faklaris Orestis, Fernandez-Rodriguez Julia, Ferrand Alexia, Gelman Laurent, Gheisari Ali, Hartmann Hella, Kukat Christian, Laude Alex, Mitkovski Miso, Munck Sebastian, North Alison J., Rasse Tobias M., Resch-Genger Ute, Schuetz Lucas C., Seitz Arne, Strambio-De-Castillia Caterina, Swedlow Jason R., Alexopoulos Ioannis, Aumayr Karin, Avilov Sergiy, Bakker Gert-Jan, Bammann Rodrigo R., Bassi Andrea, Beckert Hannes, Beer Sebastian, Belyaev Yury, Bierwagen Jakob, Birngruber Konstantin A., Bosch Manel, Breitlow Juergen, Cameron Lisa A., Chalfoun Joe, Chambers James J., Chen Chieh-Li, Conde-Sousa Eduardo, Corbett Alexander D., Cordelieres Fabrice P., Del Nery Elaine, Dietzel Ralf, Eismann Frank, Fazeli Elnaz, Felscher Andreas, Fried Hans, Gaudreault Nathalie, Goh Wah Ing, Guilbert Thomas, Hadleigh Roland, Hemmerich Peter, Holst Gerhard A., Itano Michelle S., Jaffe Claudia B., Jambor Helena K., Jarvis Stuart C., Keppler Antje, Kirchenbuechler David, Kirchner Marcel, Kobayashi Norio, Krens Gabriel, Kunis Susanne, Lacoste Judith, Marcello Marco, Martins Gabriel G., Metcalf Daniel J., Mitchell Claire A., Moore Joshua, Mueller Tobias, Nelson Michael S., Ogg Stephen, Onami Shuichi, Palmer Alexandra L., Paul-Gilloteaux Perrine, Pimentel Jaime A., Plantard Laure, Podder Santosh, Rexhepaj Elton, Royon Arnaud, Saari Markku A., Schapman Damien, Schoonderwoert Vincent, Schroth-Diez Britta, Schwartz Stanley, Shaw Michael, Spitaler Martin, Stoeckl Martin T., Sudar Damir, Teillon Jeremie, Terjung Stefan, Thuenauer Roland, Wilms Christian D., Wright Graham D., Nitschke Roland
Publisher: WILEY
Publication year: 2021
Journal: Journal of Microscopy
Journal name in source: JOURNAL OF MICROSCOPY
Journal acronym: J MICROSC-OXFORD
Volume: 284
Issue: 1
First page : 56
Last page: 73
Number of pages: 18
ISSN: 0022-2720
DOI: https://doi.org/10.1111/jmi.13041(external)
Web address : https://doi.org/10.1111/jmi.13041(external)
Self-archived copy’s web address: https://research.utu.fi/converis/portal/detail/Publication/66932122(external)
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.
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