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 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 datametrics.
Highlights
Current Situation Since their introduction in the early 17th Century, microscopes have transitioned from basic, qualitative image-collecting tools to sophisticated instruments capable of automatically acquiring information-rich images that are further processed via advanced image processing and analysis steps to extract quantitative information about the underlying science
The first step will be to reach a consensus between microscope and system component manufacturers, users, and microscope custodians regarding precisely what needs to be measured, how, and at what frequency, taking into account the experiment being performed and the downstream image analysis strategy
The microscope manufacturers can provide some of these as internal QC tools that align with the QUAREP-LiMi guidelines, thereby facilitating rapid, simple measurements by all microscope users and custodians
Summary
Current Situation Since their introduction in the early 17th Century, microscopes have transitioned from basic, qualitative image-collecting tools to sophisticated instruments capable of automatically acquiring information-rich images that are further processed via advanced image processing and analysis steps to extract quantitative information about the underlying science. WG11 will focus on the following activities: 1) inform scientific publishers of the standards and metadata put forward by the other QUAREP Working Groups; 2) liaise with and encourage individual journals to modify their imaging guidelines to align with these recommendations; 3) work together with the scientific publishers to enforce high standards of imaging metadata reporting in all research works r https://www.bioimagingna.org/qc-dm-wg accepted for publication; 4) facilitate the involvement of technical reviewers with significant microscopy expertise during the review of papers that rely heavily on imaging techniques; 5) work together with publishers to promote and increase the appropriate acknowledgement and co-authorship of imaging scientists and core imaging facilities in publications; 6) encourage publishers to compel authors to make raw imaging data available if, and when, required for validation of published research and to make reasonable suggestions regarding duration of storage of raw imaging data relevant to published results; 7) propose minimum standards for figure quality, figure colour selection, scale bars, inserts, annotations and labelling, in order to render all microscopy figures interpretable by experts and non-experts alike. It will cover the vast majority of current microscopy-based research
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