. 2021 Dec;18(12):1423-1426.

doi: 10.1038/s41592-021-01162-y.

QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

Ulrike Boehm^#¹, Glyn Nelson^#², Claire M Brown^#³, Steve Bagley⁴, Peter Bajcsy⁵, Johanna Bischof⁶, Aurelien Dauphin⁷, Ian M Dobbie⁸, John E Eriksson⁹, Orestis Faklaris¹⁰, Julia Fernandez-Rodriguez¹¹, Alexia Ferrand¹², Laurent Gelman¹³, Ali Gheisari¹⁴, Hella Hartmann¹⁴, Christian Kukat¹⁵, Alex Laude², Miso Mitkovski¹⁶, Sebastian Munck^{17

18

19}, Alison J North²⁰, Tobias M Rasse²¹, Ute Resch-Genger²², Lucas C Schuetz²³, Arne Seitz²⁴, Caterina Strambio-De-Castillia²⁵, Jason R Swedlow²⁶, Roland Nitschke^{27

28}

Affiliations

¹ Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
² Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK.
³ Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada.
⁴ Visualisation, Irradiation & Analysis, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield, UK.
⁵ National Institute of Standards and Technology, Gaithersburg, MD, USA.
⁶ Euro-BioImaging ERIC, Heidelberg, Germany.
⁷ Unite Génétique et Biologie du Développement U934, PICT-IBiSA, Institut Curie/Inserm/CNRS/PSL Research University, Paris, France.
⁸ Department of Biochemistry, University of Oxford, Oxford, UK.
⁹ Turku Bioscience Centre, Euro-Bioimaging ERIC, Turku, Finland.
¹⁰ BCM, University of Montpellier, CNRS, INSERM, Montpellier, France.
¹¹ Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
¹² Imaging Core Facility Biozentrum, University of Basel, Basel, Switzerland.
¹³ Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
¹⁴ Light Microscopy Facility, CMCB Technology Platform, TU Dresden, Dresden, Germany.
¹⁵ FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany.
¹⁶ Light Microscopy Facility, Max Planck Institute of Experimental Medicine, Goettingen, Germany.
¹⁷ VIB BioImaging Core, Leuven, Flanders, Belgium.
¹⁸ VIB-KU Leuven Center for Brain and Disease, Leuven, Flanders, Belgium.
¹⁹ KU Leuven Department for Neuroscience, Leuven, Flanders, Belgium.
²⁰ The Rockefeller University, New York, NY, USA.
²¹ Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
²² Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany.
²³ European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany.
²⁴ Faculty of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
²⁵ Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
²⁶ Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
²⁷ Life Imaging Center, Albert-Ludwigs University, Freiburg, Germany. Roland.Nitschke@uni-freiburg.de.
²⁸ Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany. Roland.Nitschke@uni-freiburg.de.

^# Contributed equally.

PMID: 34021279
PMCID: PMC9443067
DOI: 10.1038/s41592-021-01162-y

QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

Ulrike Boehm et al. Nat Methods. 2021 Dec.

. 2021 Dec;18(12):1423-1426.

doi: 10.1038/s41592-021-01162-y.

Authors

Affiliations

¹ Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
² Bioimaging Unit, Newcastle University, Newcastle upon Tyne, UK.
³ Advanced BioImaging Facility (ABIF), McGill University, Montreal, Quebec, Canada.
⁴ Visualisation, Irradiation & Analysis, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield, UK.
⁵ National Institute of Standards and Technology, Gaithersburg, MD, USA.
⁶ Euro-BioImaging ERIC, Heidelberg, Germany.
⁷ Unite Génétique et Biologie du Développement U934, PICT-IBiSA, Institut Curie/Inserm/CNRS/PSL Research University, Paris, France.
⁸ Department of Biochemistry, University of Oxford, Oxford, UK.
⁹ Turku Bioscience Centre, Euro-Bioimaging ERIC, Turku, Finland.
¹⁰ BCM, University of Montpellier, CNRS, INSERM, Montpellier, France.
¹¹ Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
¹² Imaging Core Facility Biozentrum, University of Basel, Basel, Switzerland.
¹³ Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
¹⁴ Light Microscopy Facility, CMCB Technology Platform, TU Dresden, Dresden, Germany.
¹⁵ FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany.
¹⁶ Light Microscopy Facility, Max Planck Institute of Experimental Medicine, Goettingen, Germany.
¹⁷ VIB BioImaging Core, Leuven, Flanders, Belgium.
¹⁸ VIB-KU Leuven Center for Brain and Disease, Leuven, Flanders, Belgium.
¹⁹ KU Leuven Department for Neuroscience, Leuven, Flanders, Belgium.
²⁰ The Rockefeller University, New York, NY, USA.
²¹ Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
²² Division Biophotonics, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany.
²³ European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany.
²⁴ Faculty of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
²⁵ Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
²⁶ Divisions of Computational Biology and Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
²⁷ Life Imaging Center, Albert-Ludwigs University, Freiburg, Germany. Roland.Nitschke@uni-freiburg.de.
²⁸ Life Imaging Center and Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany. Roland.Nitschke@uni-freiburg.de.

^# Contributed equally.

PMID: 34021279
PMCID: PMC9443067
DOI: 10.1038/s41592-021-01162-y

Erratum in

Author Correction: QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy.
Boehm U, Nelson G, Brown CM, Bagley S, Bajcsy P, Bischof J, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Nitschke R. Boehm U, et al. Nat Methods. 2022 Feb;19(2):256. doi: 10.1038/s41592-021-01387-x. Nat Methods. 2022. PMID: 34980905 No abstract available.

Abstract

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, image acquisition, management and analysis.

PubMed Disclaimer

Conflict of interest statement

Competing interests

The authors declare no competing interests.

Figures

**Figure 1.**
Overview of topics and aims covered by QUAREP-LiMi initiative QUAREP-LiMi aims to define standard operating procedures and tools for device monitoring, benchmarking and quality management of light microscopy instruments and images, that are aligned with existing ISO standards, as well as to develop in liaison with ISO or other stakeholders (corporate partners, funders and publishers) a community based consensus around microscope and image data QC.

See this image and copyright information in PMC

References

1. Baker M Reproducibility crisis: Blame it on the antibodies. Nature 521, 274–276, (2015). - PubMed
1. Bordeaux J, Welsh A, Agarwal S, Killiam E, Baquero M, Hanna J, Anagnostou V & Rimm D Antibody validation. Biotechniques 48, 197–209, (2010). - PMC - PubMed
1. Eckers JC, Swick AD & Kimple RJ Identity Crisis - Rigor and Reproducibility in Human Cell Lines. Radiat Res 189, 551–552, (2018). - PMC - PubMed
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1. Hutson M Artificial intelligence faces reproducibility crisis. Science 359, 725–726, (2018). - PubMed

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QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

Affiliations

QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

Authors

Affiliations

Erratum in

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources