TY - JOUR A1 - Nelson, G. A1 - Boehm, U. A1 - Bagley, S. A1 - Bajcsy, P. A1 - Bischof, J. A1 - Brown, C. M. A1 - Dauphin, A. A1 - Dobbie, I. M. A1 - Eriksson, J. E. A1 - Faklaris, O. A1 - Fernandez-Rodriguez, J. A1 - Ferrand, A. A1 - Gelman, L, A1 - Gheisari, A. A1 - Hartmann, H. A1 - Kukat, C. A1 - Laude, A. A1 - Mitkovski, M. A1 - Munck, S. A1 - North, A. J. A1 - Rasse, T. A1 - Resch-Genger, Ute A1 - Schuetz, L. C. A1 - Seitz, A. A1 - Strambio-De-Castillia, C. A1 - Swedlow, J. R. A1 - Alexopoulos, I. A1 - Aumayr, K. A1 - Avilov, S. A1 - Bakker, G.-J. A1 - Bammann, R. R. A1 - Bassi, A. A1 - Beckert, H. A1 - Beer, S. A1 - Belyaev, Y. A1 - Bierwagen, J. A1 - Birngruber, K. A. A1 - Bosch, M. A1 - Breitlow, J. A1 - Cameron, L. A. A1 - Chalfoun, J. A1 - Chambers, J. J. A1 - Chen, C.-L. A1 - Conde-Sousa, E. A1 - Corbett, A. D. A1 - Cordelieres, F. P. A1 - Del Nery, E. A1 - Dietzel, R. A1 - Eismann, F. A1 - Fazeli, E. A1 - Felscher, A. A1 - Fried, H. A1 - Gaudreault, N. A1 - Goh, W. I. A1 - Guilbert, T. A1 - Hadleigh, R. A1 - Hemmerich, P. A1 - Holst, G. A. A1 - Itano, M. S. A1 - Jaffe, C. B. A1 - Jambor, H. K. A1 - Jarvis, S. C. A1 - Keppler, A. A1 - Kirchenbuechler, D. A1 - Kirchner, M. A1 - Kobayashi, N. A1 - Krens, G. A1 - Kunis, S. A1 - Lacoste, J. A1 - Marcello, M. A1 - Martins, G. G. A1 - Metcalf, D. J. A1 - Mitchell, C. A. A1 - Moore, J. A1 - Mueller, T. A1 - Nelson, M. S. A1 - Ogg, S. A1 - Onami, S. A1 - Palmer, A. L. A1 - Paul-Gilloteaux, P. A1 - Pimentel, J. A. A1 - Plantard, L. A1 - Podder, S. A1 - Rexhepaj, E. A1 - Royon, A. A1 - Saari, M. A. A1 - Schapman, D. A1 - Schoonderwoert, V. A1 - Schroth-Diez, B. A1 - Schwartz, S. A1 - Shaw, M. A1 - Spitaler, M. A1 - Stoeckl, M. T. A1 - Sudar, D. A1 - Teillon, J. A1 - Terjung, S. A1 - Thuenauer, R. A1 - Wilms, C. D. A1 - Wright, G. D. A1 - Nitschke, R. T1 - QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy JF - Journal of microscopy N2 - 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 QUAREPLiMi 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. KW - Fluorescence KW - Microscopy KW - Quality assurance KW - Comparability KW - Imaging KW - Standards KW - Reference materials KW - Reliability KW - Data KW - Reference data KW - Biology KW - Medicine KW - Life science PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-530629 DO - https://doi.org/10.1111/jmi.13041 SN - 1365-2818 VL - 284 IS - 1 SP - 56 EP - 73 PB - Wiley-Blackwell CY - Oxford AN - OPUS4-53062 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Brand, U. A1 - Beckert, E. A1 - Beutler, A. A1 - Dai, G. A1 - Stelzer, C. A1 - Hertwig, Andreas A1 - Klapetek, P. A1 - Koglin, J. A1 - Thelen, R. A1 - Tutsch, R. T1 - Comparison of optical and tactile layer thickness measurements of polymers and metals on silicon or SiO2 JF - Measurement science and technology N2 - The thickness measurement of transparent layers with optical techniques is very problematic. The observed deviations can easily reach 100% of the layer thickness to be measured. In order to analyse these deviations, tactile reference measurements have been developed. The proposed method is based on contact mode measurements with low contact pressure. With stylus instruments, this can be realized either by using the recommended tip radius of 2 µm and very small probing forces in the micronewton range (and low scanning speeds of 50 µm s-1) or by using the recommended probing force of 750 µN, but a large probing tip radius. Three metal layers on silicon or silicon dioxide and two polymer resist materials on a thin chromium adhesive layer on silicon are used as artefacts. The comparison of the optical measurements with the tactile reference values disclosed deviations of the optical measurements of up to 195% of the layer thickness. Layer thicknesses were between 200 nm and 4 µm. This paper analyses the deviations of two white light interference microscopes, one phase shift interference microscope, one confocal microscope, one autofocus sensor, a chromatic sensor, an interferometric film thickness sensor and one spectroscopic ellipsometer. Simple and well-known expressions for the description of the observed deviations are presented and discussed. The order of magnitude of the observed deviations can be described well by these correction formulas but further investigations are necessary in order to better understand the systematic deviations of optical surface measuring instruments on non-cooperating surfaces. KW - Layer thickness KW - Stylus instrument KW - Deformation KW - Polymer KW - Silicon KW - Silicon dioxide PY - 2011 DO - https://doi.org/10.1088/0957-0233/22/9/094021 SN - 0957-0233 SN - 1361-6501 VL - 22 IS - 094021 SP - 094021-1 - 094021-14 PB - IOP Publ. Ltd. CY - Bristol AN - OPUS4-24701 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -