QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
Glyn Nelson,Ulrike Boehm,Steve Bagley,Peter Bajcsy,Johanna Bischof,Claire M. Brown,Aurelien Dauphin,Ian M. Dobbie,John E Eriksson,Orestis Faklaris,Julia Fernandez-Rodriguez,Alexia Ferrand,Laurent Gelman,Ali Gheisari,Hella Hartmann,Christian Kukat,Alex Laude,Miso Mitkovski,Sebastian Munck,Alison J. North,Tobias M. Rasse,Ute Resch-Genger,Lucas C Schuetz,Arne Seitz,Caterina Strambio-De-Castillia,Jason R. Swedlow,Ioannis Alexopoulos,Karin Aumayr,Sergiy V. Avilov,Gert-Jan Bakker,Rodrigo R Bammann,Andrea Bassi,Hannes Beckert,Sebastian Beer,Yury Belyaev,Jakob Bierwagen,Konstantin A Birngruber,Manel Bosch,Juergen Breitlow,Lisa A. Cameron,Joe Chalfoun,James J. Chambers,Chieh-Li Chen,Eduardo Conde-Sousa,Alexander D. Corbett,Fabrice P. Cordelières,Elaine Del Nery,Ralf Dietzel,Frank Eismann,Elnaz Fazeli,Andreas Felscher,Hans-Ulrich Fried,Nathalie Gaudreault,Wah Ing Goh,Thomas Guilbert,Roland Hadleigh,Peter Hemmerich,Gerhard A Holst,Michelle S. Itano,Claudia B Jaffe,Helena Jambor,Stuart C Jarvis,Antje Keppler,David Kirchenbuechler,Marcel Kirchner,Norio Kobayashi,Gabriel Krens,Susanne Kunis,Judith Lacoste,Marco Marcello,Gabriel G. Martins,Daniel J Metcalf,Claire A. Mitchell,Joshua Moore,Tobias Mueller,Michael S. Nelson,Stephen Ogg,Shuichi Onami,Alexandra L Palmer,Perrine Paul-Gilloteaux,Jaime A. Pimentel,Laure Plantard,Santosh Podder,Elton Rexhepaj,Arnaud Royon,Markku Saari,Damien Schapman,Vincent Schoonderwoert,Britta Schroth-Diez,Stanley Schwartz,Michael Shaw,Martin Spitaler,Martin T Stoeckl,Damir Sudar,Jeremie Teillon,Stefan Terjung,Roland Thuenauer,Christian D Wilms,Graham D. Wright,Roland Nitschke +99 more
TLDR
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.read more
Citations
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Volume electron microscopy
Christopher J. Peddie,Christel Genoud,Anna Kreshuk,Kimberly Meechan,Kristina D. Micheva,Kedar Narayan,Constantin Pape,Robert G. Parton,Nicole L. Schieber,Yannick Schwab,B. Titze,Paul Verkade,Aubrey V. Weigel,Lucy M. Collinson +13 more
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MITI minimum information guidelines for highly multiplexed tissue images
TL;DR: The Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard as mentioned in this paper applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology.
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Open microscopy in the life sciences: quo vadis?
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Open microscopy in the life sciences: Quo Vadis?.
Johannes Hohlbein,Madeline Yung,Benedict Diederich,Barbora Marsikova,Emmanuel G. Reynaud,Seamus Holden,Wiebke Jahr,Robert Haase,Kirti Prakash +8 more
TL;DR: In this article, the authors argue that the availability of well-designed open hardware and software solutions targeting broad user groups or even non-experts will increasingly be relevant to cope with the increasing complexity of cutting-edge imaging technologies.
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Live cell microscopy: From image to insight
TL;DR: This review aims to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment and puts a particular focus on yeast, but many of the concepts discussed are applicable also to other organisms.
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Metadata matters: access to image data in the real world
Melissa Linkert,Curtis Rueden,Chris Allan,Jean-Marie Burel,William J. Moore,Andrew J. Patterson,Brian Loranger,Josh Moore,Carlos H. Neves,Donald MacDonald,Aleksandra Tarkowska,J Caitlin Sticco,Emma Hill,Mike Rossner,Kevin W. Eliceiri,Jason R. Swedlow +15 more
TL;DR: An open standard format for multidimensional microscopy image data is described and it is called on the community to use open image data standards and to insist that all imaging platforms support these file formats.