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

Ulrike Boehm; Glyn Nelson; Claire M Brown; Steve Bagley; Peter Bajcsy; Johanna Bischof; Aurelien Dauphin; Ian M Dobbie; John E Eriksson; Orestis Faklaris; Julia Fernandez-Rodriguez; Alexia Ferrand; Laurent Gelman; Ali Gheisari; Hella Hartmann; Christian Kukat; Alex Laude; Miso Mitkovski; Sebastian Munck; Alison J North; Tobias M Rasse; Ute Resch-Genger; Lucas C Schuetz; Arne Seitz; Caterina Strambio-De-Castillia; Jason R Swedlow; Roland Nitschke

doi:10.1038/s41592-021-01162-y

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

Nat Methods. 2021 Dec;18(12):1423-1426. doi: 10.1038/s41592-021-01162-y.

Authors

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.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Biomedical Research / organization & administration
Calibration
Humans
Image Processing, Computer-Assisted / methods*
Metadata
Microscopy / instrumentation*
Microscopy / methods*
Microscopy / standards*
Quality Control
Reproducibility of Results
Software

Grants and funding

U01 CA200059/CA/NCI NIH HHS/United States