--- _id: '9911' abstract: - lang: eng text: 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. acknowledgement: We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg. article_processing_charge: Yes article_type: original author: - first_name: Glyn full_name: Nelson, Glyn last_name: Nelson - first_name: Ulrike full_name: Boehm, Ulrike last_name: Boehm - first_name: Steve full_name: Bagley, Steve last_name: Bagley - first_name: Peter full_name: Bajcsy, Peter last_name: Bajcsy - first_name: Johanna full_name: Bischof, Johanna last_name: Bischof - first_name: Claire M. full_name: Brown, Claire M. last_name: Brown - first_name: Aurélien full_name: Dauphin, Aurélien last_name: Dauphin - first_name: Ian M. full_name: Dobbie, Ian M. last_name: Dobbie - first_name: John E. full_name: Eriksson, John E. last_name: Eriksson - first_name: Orestis full_name: Faklaris, Orestis last_name: Faklaris - first_name: Julia full_name: Fernandez-Rodriguez, Julia last_name: Fernandez-Rodriguez - first_name: Alexia full_name: Ferrand, Alexia last_name: Ferrand - first_name: Laurent full_name: Gelman, Laurent last_name: Gelman - first_name: Ali full_name: Gheisari, Ali last_name: Gheisari - first_name: Hella full_name: Hartmann, Hella last_name: Hartmann - first_name: Christian full_name: Kukat, Christian last_name: Kukat - first_name: Alex full_name: Laude, Alex last_name: Laude - first_name: Miso full_name: Mitkovski, Miso last_name: Mitkovski - first_name: Sebastian full_name: Munck, Sebastian last_name: Munck - first_name: Alison J. full_name: North, Alison J. last_name: North - first_name: Tobias M. full_name: Rasse, Tobias M. last_name: Rasse - first_name: Ute full_name: Resch-Genger, Ute last_name: Resch-Genger - first_name: Lucas C. full_name: Schuetz, Lucas C. last_name: Schuetz - first_name: Arne full_name: Seitz, Arne last_name: Seitz - first_name: Caterina full_name: Strambio-De-Castillia, Caterina last_name: Strambio-De-Castillia - first_name: Jason R. full_name: Swedlow, Jason R. last_name: Swedlow - first_name: Ioannis full_name: Alexopoulos, Ioannis last_name: Alexopoulos - first_name: Karin full_name: Aumayr, Karin last_name: Aumayr - first_name: Sergiy full_name: Avilov, Sergiy last_name: Avilov - first_name: Gert Jan full_name: Bakker, Gert Jan last_name: Bakker - first_name: Rodrigo R. full_name: Bammann, Rodrigo R. last_name: Bammann - first_name: Andrea full_name: Bassi, Andrea last_name: Bassi - first_name: Hannes full_name: Beckert, Hannes last_name: Beckert - first_name: Sebastian full_name: Beer, Sebastian last_name: Beer - first_name: Yury full_name: Belyaev, Yury last_name: Belyaev - first_name: Jakob full_name: Bierwagen, Jakob last_name: Bierwagen - first_name: Konstantin A. full_name: Birngruber, Konstantin A. last_name: Birngruber - first_name: Manel full_name: Bosch, Manel last_name: Bosch - first_name: Juergen full_name: Breitlow, Juergen last_name: Breitlow - first_name: Lisa A. full_name: Cameron, Lisa A. last_name: Cameron - first_name: Joe full_name: Chalfoun, Joe last_name: Chalfoun - first_name: James J. full_name: Chambers, James J. last_name: Chambers - first_name: Chieh Li full_name: Chen, Chieh Li last_name: Chen - first_name: Eduardo full_name: Conde-Sousa, Eduardo last_name: Conde-Sousa - first_name: Alexander D. full_name: Corbett, Alexander D. last_name: Corbett - first_name: Fabrice P. full_name: Cordelieres, Fabrice P. last_name: Cordelieres - first_name: Elaine Del full_name: Nery, Elaine Del last_name: Nery - first_name: Ralf full_name: Dietzel, Ralf last_name: Dietzel - first_name: Frank full_name: Eismann, Frank last_name: Eismann - first_name: Elnaz full_name: Fazeli, Elnaz last_name: Fazeli - first_name: Andreas full_name: Felscher, Andreas last_name: Felscher - first_name: Hans full_name: Fried, Hans last_name: Fried - first_name: Nathalie full_name: Gaudreault, Nathalie last_name: Gaudreault - first_name: Wah Ing full_name: Goh, Wah Ing last_name: Goh - first_name: Thomas full_name: Guilbert, Thomas last_name: Guilbert - first_name: Roland full_name: Hadleigh, Roland last_name: Hadleigh - first_name: Peter full_name: Hemmerich, Peter last_name: Hemmerich - first_name: Gerhard A. full_name: Holst, Gerhard A. last_name: Holst - first_name: Michelle S. full_name: Itano, Michelle S. last_name: Itano - first_name: Claudia B. full_name: Jaffe, Claudia B. last_name: Jaffe - first_name: Helena K. full_name: Jambor, Helena K. last_name: Jambor - first_name: Stuart C. full_name: Jarvis, Stuart C. last_name: Jarvis - first_name: Antje full_name: Keppler, Antje last_name: Keppler - first_name: David full_name: Kirchenbuechler, David last_name: Kirchenbuechler - first_name: Marcel full_name: Kirchner, Marcel last_name: Kirchner - first_name: Norio full_name: Kobayashi, Norio last_name: Kobayashi - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Susanne full_name: Kunis, Susanne last_name: Kunis - first_name: Judith full_name: Lacoste, Judith last_name: Lacoste - first_name: Marco full_name: Marcello, Marco last_name: Marcello - first_name: Gabriel G. full_name: Martins, Gabriel G. last_name: Martins - first_name: Daniel J. full_name: Metcalf, Daniel J. last_name: Metcalf - first_name: Claire A. full_name: Mitchell, Claire A. last_name: Mitchell - first_name: Joshua full_name: Moore, Joshua last_name: Moore - first_name: Tobias full_name: Mueller, Tobias last_name: Mueller - first_name: Michael S. full_name: Nelson, Michael S. last_name: Nelson - first_name: Stephen full_name: Ogg, Stephen last_name: Ogg - first_name: Shuichi full_name: Onami, Shuichi last_name: Onami - first_name: Alexandra L. full_name: Palmer, Alexandra L. last_name: Palmer - first_name: Perrine full_name: Paul-Gilloteaux, Perrine last_name: Paul-Gilloteaux - first_name: Jaime A. full_name: Pimentel, Jaime A. last_name: Pimentel - first_name: Laure full_name: Plantard, Laure last_name: Plantard - first_name: Santosh full_name: Podder, Santosh last_name: Podder - first_name: Elton full_name: Rexhepaj, Elton last_name: Rexhepaj - first_name: Arnaud full_name: Royon, Arnaud last_name: Royon - first_name: Markku A. full_name: Saari, Markku A. last_name: Saari - first_name: Damien full_name: Schapman, Damien last_name: Schapman - first_name: Vincent full_name: Schoonderwoert, Vincent last_name: Schoonderwoert - first_name: Britta full_name: Schroth-Diez, Britta last_name: Schroth-Diez - first_name: Stanley full_name: Schwartz, Stanley last_name: Schwartz - first_name: Michael full_name: Shaw, Michael last_name: Shaw - first_name: Martin full_name: Spitaler, Martin last_name: Spitaler - first_name: Martin T. full_name: Stoeckl, Martin T. last_name: Stoeckl - first_name: Damir full_name: Sudar, Damir last_name: Sudar - first_name: Jeremie full_name: Teillon, Jeremie last_name: Teillon - first_name: Stefan full_name: Terjung, Stefan last_name: Terjung - first_name: Roland full_name: Thuenauer, Roland last_name: Thuenauer - first_name: Christian D. full_name: Wilms, Christian D. last_name: Wilms - first_name: Graham D. full_name: Wright, Graham D. last_name: Wright - first_name: Roland full_name: Nitschke, Roland last_name: Nitschke citation: ama: 'Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73. doi:10.1111/jmi.13041' apa: 'Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041' chicago: 'Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.' ieee: 'G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp. 56–73, 2021.' ista: 'Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.' mla: 'Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:10.1111/jmi.13041.' short: G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73. date_created: 2021-08-15T22:01:29Z date_published: 2021-08-11T00:00:00Z date_updated: 2023-08-11T10:30:40Z day: '11' department: - _id: Bio doi: 10.1111/jmi.13041 external_id: isi: - '000683702700001' intvolume: ' 284' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/jmi.13041 month: '08' oa: 1 oa_version: Published Version page: 56-73 publication: Journal of Microscopy publication_identifier: eissn: - 1365-2818 issn: - 0022-2720 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 284 year: '2021' ...