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 - Westwood, S. A1 - Josephs, R. A1 - Choteau, T. A1 - Daireaux, A. A1 - Stoppacher, N. A1 - Wielgosz, R. A1 - Davies, S. A1 - do Rego, E. A1 - Wollinger, W. A1 - Garrido, B. A1 - Fernandes, J. A1 - Lima, J. A1 - Oliveira, R. A1 - de Sena, R. A1 - Windust, A. A1 - Huang, T. A1 - Dai, X. A1 - Quan, C. A1 - He, H. A1 - Zhang, W. A1 - Wei, C. A1 - Li, N. A1 - Gao, D. A1 - Liu, Z. A1 - Lo, M. A1 - Wong, W. A1 - Pfeifer, Dietmar A1 - Koch, Matthias A1 - Dorgerloh, Ute A1 - Rothe, Robert A1 - Philipp, Rosemarie A1 - Hanari, N. A1 - Rezali, M. A1 - Arzate, C. A1 - Berenice, M. A1 - Caballero, V. A1 - Osuna, M. A1 - Krylov, A. A1 - Kharitonov, S. A1 - Lopushanskaya, E. A1 - Liu, Q. A1 - Lin, T. A1 - Fernandes-Whaley, M. A1 - Quinn, L. A1 - Nhlapo, N. A1 - Prevoo-Franzsen, D. A1 - Archer, M. A1 - Kim, B. A1 - Baek, S. A1 - Lee, S. A1 - Lee, J. A1 - Marbumrung, S. A1 - Kankaew, P. A1 - Chaorenpornpukdee, K. A1 - Chaipet, T. A1 - Shearman, K. A1 - Gören, A. A1 - Gündüz, S. A1 - Yilmaz, H. A1 - Un, I. A1 - Bilsel, G. A1 - Clarkson, C. A1 - Bedner, M. A1 - Camara, J. A1 - Lang, B. A1 - Lippa, K. A1 - Nelson, M. A1 - Toman, B. A1 - Yu, L. T1 - Mass fraction assignment of folic acid in a high purity material - CCQM-K55.d (Folic acid) Final Report JF - Metrologia N2 - The comparison required the assignment of the mass fraction of folic acid present as the main component in the comparison sample. Performance in the comparison is representative of a laboratory's measurement capability for the purity assignment of organic compounds of medium structural complexity [molecular weight range 300–500] and high polarity (pKOW < −2). Methods used by the eighteen participating NMIs or DIs were based on a mass balance (summation of impurities) or qNMR approach, or the combination of data obtained using both methods. The qNMR results tended to give slightly lower values for the content of folic acid, albeit with larger associated uncertainties, compared with the results obtained by mass balance procedures. Possible reasons for this divergence are discussed in the report, without reaching a definitive conclusion as to their origin. The comparison demonstrates that for a structurally complex polar organic compound containing a high water content and presenting a number of additional analytical challenges, the assignment of the mass fraction content property value of the main component can reasonably be achieved with an associated relative standard uncertainty in the assigned value of 0.5% KW - CCQM key comparison KW - Purity assessment KW - Folic acid PY - 2018 UR - https://www.bipm.org/utils/common/pdf/final_reports/QM/K55/CCQM-K55.d.pdf DO - https://doi.org/10.1088/0026-1394/55/1A/08013 VL - 55 IS - Technical Supplement, 2018 SP - 08013, 1 EP - 38 PB - Institute of Physics Publishing (IOP) ; Bureau International des Poids et Mesures AN - OPUS4-44999 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - George, Janine A1 - Petretto, G. A1 - Naik, Aakash Ashok A1 - Esters, M. A1 - Jackson, A. J. A1 - Nelson, R. A1 - Dronskowski, R. A1 - Rignanese, G.-M. A1 - Hautier, G. T1 - Automated bonding analysis with crystal orbital Hamilton populuations JF - ChemPlusChem N2 - Automated bonding analysis software has been developed based on Crystal Orbital Hamilton Populations to facilitate high-throughput bonding analysis and machine-learning of bonding features. This work presents the software and discusses its applications to simple and complex materials such as GaN, NaCl, the oxynitrides XTaO2N (X=Ca, Ba, Sr) and Yb14Mn1Sb11. KW - Chemical bonds KW - Automation KW - High-throughput PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-551641 DO - https://doi.org/10.1002/cplu.202200123 SN - 2192-6506 SP - 1 EP - 11 PB - Wiley-VCH CY - Weinheim AN - OPUS4-55164 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - George, Janine A1 - Petretto, G. A1 - Naik, Aakash Ashok A1 - Esters, M. A1 - Jackson, A. J. A1 - Nelson, R. A1 - Dronskowski, R. A1 - Rignanese, G.-M. A1 - Hautier, G. T1 - Automated bonding analysis with crystal orbital Hamilton populations (program code LobsterPy) N2 - This is the code for the program LobsterPy that can be used to automatically analyze and plot outputs of the program Lobster. KW - Automation KW - High-throughput computations KW - Bonding analysis PY - 2022 UR - https://doi.org/10.5281/zenodo.6320074 UR - https://doi.org/10.5281/zenodo.6415169 UR - https://doi.org/10.5281/zenodo.6415336 UR - https://doi.org/10.5281/zenodo.6581118 DO - https://doi.org/10.5281/zenodo.6320073 PB - Zenodo CY - Geneva AN - OPUS4-55174 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Boehm, U. A1 - Nelson, G. A1 - Brown, C. M. A1 - Bagley, S. A1 - Bajcsy, P. A1 - Bischof, J. 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. M. A1 - Resch-Genger, Ute A1 - Schuetz, L. C. A1 - Seitz, A. A1 - Strambio-De-Castillia, C. A1 - Swedlow, J. R. A1 - Nitschke, R. T1 - Author correction: QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy T2 - Nature methods N2 - This is a corrigendum to the original article "QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy" that was published in the journal "Nature methods", vol. 18 (2021), pp. 1424-1427. PY - 2022 DO - https://doi.org/10.1038/s41592-021-01387-x SN - 1548-7105 SP - 1 PB - Nature Publishing Group CY - London AN - OPUS4-54270 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Boehm, U. A1 - Nelson, G. A1 - Brown, C. M. A1 - Bagley, S. A1 - Bajcsy, P. A1 - Bischof, J. 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. M. A1 - Resch-Genger, Ute A1 - Schuetz, L. C. A1 - Seitz, A. A1 - Strambio-De-Castillia, C. A1 - Swedlow, J. R. A1 - Nitschke, R. T1 - QUAREP-LiMi: A community endeavor to advance quality assessment and reproducibility in light microscopy JF - Nature methods N2 - The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through Quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for Hardware calibration and image acquisition, management and analysis. 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 DO - https://doi.org/10.1038/s41592-021-01162-y SN - 1548-7105 VL - 18 SP - 1424 EP - 1427 PB - Nature Publishing Group CY - London AN - OPUS4-52722 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - George, Janine A1 - Petretto, G. A1 - Naik, Aakash Ashok A1 - Esters, M. A1 - Jackson, A. J. A1 - Nelson, R. A1 - Dronskowski, R. A1 - Rignanese, G.-M. A1 - Hautier, G. T1 - Cover profile for the article "Automated bonding analysis with crystal orbital Hamilton populuations" JF - ChemPlusChem N2 - Invited for this month’s cover are researchers from Bundesanstalt für Materialforschung und -prüfung (Federal Institute for Materials Research and Testing) in Germany, Friedrich Schiller University Jena, Université catholique de Louvain, University of Oregon, Science & Technology Facilities Council, RWTH Aachen University, Hoffmann Institute of Advanced Materials, and Dartmouth College. The cover picture shows a workflow for automatic bonding analysis with Python tools (green python). The bonding analysis itself is performed with the program LOBSTER (red lobster). The starting point is a crystal structure, and the results are automatic assessments of the bonding situation based on Crystal Orbital Hamilton Populations (COHP), including automatic plots and text outputs. Coordination environments and charges are also assessed. More information can be found in the Research Article by J. George, G. Hautier, and co-workers. KW - Automation KW - Chemical bonds KW - High-throughput PY - 2022 DO - https://doi.org/10.1002/cplu.202200246 SN - 2192-6506 SP - 1 EP - 2 PB - Wiley-VCH CY - Weinheim AN - OPUS4-55557 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -