QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

Autor(en): Nelson, Glyn
Boehm, Ulrike
Bagley, Steve
Bajcsy, Peter
Bischof, Johanna
Brown, Claire M.
Dauphin, Aurelien
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
Stichwörter: confocal; light microscopy; metadata; Microscopy; MINIMUM INFORMATION; quality assessment; quality control; reproducibility; RESOLUTION; widefield
Erscheinungsdatum: 2021
Herausgeber: WILEY
Volumen: 284
Ausgabe: 1
Startseite: 56
Seitenende: 73
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.
ISSN: 00222720
DOI: 10.1111/jmi.13041

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