QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy.
QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy.
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DOI：
10.1111/jmi.13041
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发表时间：
2021-10
影响因子：
2
通讯作者：
Nitschke, Roland
中科院分区：
文献类型：
--
作者：
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
现代光学显微镜已经从一种主要用于进行经验观察的工具发展成为一种复杂的定量设备，是物理和生命科学研究的一个组成部分。如今，几乎每个实验室都有显微镜。然而，尽管它们普遍用于捕获和量化科学现象，但无论是对定量成像技术的基本原理的透彻理解，还是对如何校准，操作和维护显微镜的适当知识，都不能被视为理所当然。在评价所获得的数据和复制科学实验方面经常遇到的广泛困难，这些困难都是有据可查的，这清楚地表明了这一点。事实上，研究表明，超过70%的研究人员尝试过重复另一位科学家的实验，但失败了，而超过一半的研究人员甚至未能重现自己的实验。在科学期刊上发表的实验再现性危机背后的一个因素是由于缺乏认识和/或缺乏对应用技术的了解而导致的成像方法的频繁低报。虽然生物医学研究中使用的一些方法的质量控制程序，如基因组学（如DNA测序，RNA-seq）或细胞计数，已被引入（如ENCODE），这个问题还没有解决光学显微镜仪器和图像。虽然已经公布了许多校准标准和协议，但对质量评估和再现性的共同标准和指南缺乏认识和一致意见。2020年4月，我们成立了光学显微镜仪器和图像质量评估和再现计划（QUAREP-LiMi）。该计划包括来自学术界和工业界的成像科学家，他们对更好地了解显微镜的性能和局限性以及改进光学显微镜的质量控制（QC）有着共同的兴趣。QUAREP-LiMi倡议的最终目标是建立一套通用的质量控制标准、指南、元数据模型和工具，包括详细的协议，最终目的是提高科学研究的可重复性进展。这份白色文件（1）总结了在该领域发现的促使QUAREP-LiMi倡议启动的主要障碍;（2）确定迫切需要通过利益相关者社区，包括研究人员、成像科学家、生物图像分析师、生物图像信息学开发人员、企业合作伙伴、资助机构、标准组织，以基层方式解决这些障碍，科学出版商和观察员;（3）概述QUAREP-LiMi倡议的当前行动;（4）提出未来可以采取的措施，以改善拟议的质量控制管理指南的传播和接受。总而言之，QUAREP-LiMi计划的主要目标是通过引入广泛接受的标准实践和准确捕获的图像数据指标来提高光学显微镜图像数据的整体质量和再现性。
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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影响因子：
48
作者：
Ellenberg J;Swedlow JR;Barlow M;Cook CE;Sarkans U;Patwardhan A;Brazma A;Birney E
通讯作者：
Birney E
影响因子：
2.8
作者：
Cole, Richard W.;Thibault, Marc;Brown, Claire M.
通讯作者：
Brown, Claire M.
影响因子：
2
作者：
Kedziora, Katarzyna M.;Prehn, Johen H. M.;Bernas, Tytus
通讯作者：
Bernas, Tytus
DOI：
10.1073/pnas.1621440114
发表时间：
2017-03-07
影响因子：
11.1
作者：
Eliscovich, Carolina;Shenoy, Shailesh M.;Singer, Robert H.
通讯作者：
Singer, Robert H.
影响因子：
2.5
作者：
Ferrando-May, Elisa;Hartmann, Hella;Reymann, Juergen;Ansari, Nariman;Utz, Nadine;Fried, Hans-Ulrich;Kukat, Christian;Peychl, Jan;Liebig, Christian;Terjung, Stefan;Laketa, Vibor;Sporbert, Anje;Weidtkamp-Peters, Stefanie;Schauss, Astrid;Zuschratter, Werner;Avilov, Sergiy
通讯作者：
Avilov, Sergiy