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Pré-Publication, Document De Travail Année : 2021

QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

Glyn Nelson (1) , Ulrike Boehm (2) , Steve Bagley (3) , Peter Bajcsy (4) , Johanna Bischof (5) , Claire M Brown (6) , Aurelien Dauphin (7) , Ian M Dobbie (8) , John E Eriksson (5) , Orestis Faklaris (9) , Julia Fernandez-Rodriguez (10) , Alexia Ferrand (11) , Laurent Gelman (12) , Ali Gheisari (13) , Hella Hartmann (13) , Christian Kukat (14) , Alex Laude (1) , Miso Mitkovski (15) , Sebastian Munck (16) , Alison J North (17) , Tobias M Rasse (18) , Ute Resch-Genger (19) , Lucas C Schuetz (20) , Arne Seitz (21) , Caterina Strambio-De-Castillia (22) , Jason R Swedlow (23) , Ioannis Alexopoulos (24) , Karin Aumayr (25) , Sergiy Avilov (26) , Gert-Jan Bakker (27) , Rodrigo R Bammann (28) , Andrea Bassi (29) , Hannes Beckert (30) , Sebastian Beer (31) , Yury Belyaev (32) , Jakob Bierwagen (28) , Konstantin A Birngruber (28) , Manel Bosch (33) , Juergen Breitlow (28) , Lisa A Cameron (34) , Joe Chalfoun (4) , James J Chambers (35) , Chieh-Li Chen (28) , Eduardo Conde-Sousa (36) , Alexander D Corbett (37) , Fabrice P Cordelieres (38) , Elaine del Nery (39) , Ralf Dietzel (28) , Frank Eismann (28) , Elnaz Fazeli (5) , Andreas Felscher (28) , Hans Fried (40) , Nathalie Gaudreault (41) , Wah Ing Goh (42) , Thomas Guilbert (43) , Roland Hadleigh (28) , Peter Hemmerich (44) , Gerhard A Holst (28) , Michelle S Itano (45) , Claudia B Jaffe (28) , Helena K Jambor (46) , Stuart C Jarvis (28) , Antje Keppler (28) , David Kirchenbuechler (47) , Marcel Kirchner (48) , Norio Kobayashi (49) , Gabriel Krens (50) , Susanne Kunis (51) , Judith Lacoste (28) , Marco Marcello (52) , Gabriel G Martins (53) , Daniel J Metcalf (28) , Claire A Mitchell (54) , Joshua Moore (23) , Tobias Mueller (55) , Michael S Nelson (56) , Stephen Ogg (57) , Shuichi Onami (58) , Alexandra L Palmer (20) , Perrine Paul-Gilloteaux (59, 60) , Jaime A Pimentel (61) , Laure Plantard (12) , Santosh Podder (62) , Elton Rexhepaj (63) , Arnaud Royon (28) , Markku A Saari (64, 5) , Damien Schapman (65) , Vincent Schoonderwoert (28) , Britta Schroth-Diez (66) , Stanley Schwartz (67) , Michael Shaw (68) , Martin Spitaler (69) , Martin T Stoeckl (70) , Damir Sudar (28) , Jeremie Teillon (38) , Stefan Terjung (21) , Roland Thuenauer (71) , Christian D Wilms (28) , Graham D Wright (42) , Roland Nitschke (72)
1 Newcastle University [Newcastle]
2 HHMI - Howard Hughes Medical Institute
3 Cancer Research UK Manchester Institute
4 NIST - National Institute of Standards and Technology [Gaithersburg]
5 University of Turku
6 McGill University = Université McGill [Montréal, Canada]
7 Génétique et Biologie du Développement
8 University of Oxford
9 BCM - BioCampus
10 Sahlgrenska Academy at University of Gothenburg [Göteborg]
11 Unibas - Université de Bâle = University of Basel = Basel Universität
12 FMI - Friedrich Miescher Institute for Biomedical Research
13 CMCB - Center for Molecular and Cellular Bioengineering [TU Dresden, Germany]
14 Max-Planck-Institut fur Biologie = Max Planck Institute for Biology [Tübingen]
15 MPI - Max Planck Institute of Experimental Medicine [Göttingen]
16 VIB [Belgium]
17 Rockefeller University [New York]
18 MPI-HLR - Max Planck Institute for Heart and Lung Research
19 BAM Bundesanstalt für Materialforschung u. -prüfung
20 The Francis Crick Institute [London]
21 EPFL - Ecole Polytechnique Fédérale de Lausanne
22 UMASS - University of Massachusetts Medical School [Worcester]
23 University of Dundee
24 Radboud University [Nijmegen]
25 IMP - Research Institute of Molecular Pathology
26 MPI-IE - Max Planck Institute of Immunobiology and Epigenetics
27 Radboud Institute for Molecular Life Sciences [Nijmegen, the Netherlands]
28 Sans affiliation
29 POLIMI - Dipartimento di Fisica [Politecnico Milano]
30 Universität Bonn = University of Bonn
31 Hamamatsu University School of Medicine
32 UNIBE - Universität Bern / University of Bern
33 UB - Universitat de Barcelona
34 Duke University [Durham]
35 UMass Amherst - University of Massachusetts [Amherst]
36 I3S - Instituto de Investigação e Inovação em Saúde
37 University of Exeter
38 BIC - Bordeaux Imaging Center
39 PICT-IBiSA - BioImaging Cell and Tissue Core Facility
40 DZNE - Deutsches Zentrum für Neurodegenerative Erkrankungen [Ulm]
41 Allen Institute [Seattle]
42 A*STAR - Agency for science, technology and research [Singapore]
43 IC UM3 (UMR 8104 / U1016) - Institut Cochin
44 FLI - Leibniz Institute on Aging - Fritz Lipmann Institute
45 UNC - University of North Carolina [Chapel Hill]
46 University Hospital Carl Gustav Carus [Dresden, Germany]
47 Northwestern University [Chicago, Ill. USA]
48 Max planck Institute for Biology of Ageing [Cologne]
49 RIKEN RAP - RIKEN Center for Advanced Photonics [Wako]
50 IST Austria - Institute of Science and Technology [Klosterneuburg, Austria]
51 University of Osnabrueck
52 University of Liverpool
53 ULISBOA - Universidade de Lisboa = University of Lisbon
54 Warwick Medical School
55 GMI - Gregor Mendel Institute of Molecular Plant Biology
56 City of Hope Comprehensive Cancer Center [Duarte]
57 University of Alberta
58 RIKEN BDR - RIKEN Center for Biosystems Dynamics Research [Kobe]
59 SFR François Bonamy - Structure fédérative de recherche François Bonamy
60 ITX - ITX - unité de recherche de l'institut du thorax
61 UNAM - Universidad Nacional Autónoma de México = National Autonomous University of Mexico
62 IISER Pune - Indian Institute of Science Education and Research Pune
63 Sanofi Aventis R&D [Chilly-Mazarin]
64 Åbo Akademi University [Turku]
65 PRIMACEN - Plate-Forme de Recherche en Imagerie Cellulaire de Haute-Normandie
66 MPI-CBG - Max Planck Institute of Molecular Cell Biology and Genetics
67 Nikon Corporation
68 NPL - National Physical Laboratory [Teddington]
69 MPIB - Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry
70 University of Konstanz
71 Heinrich Pette Institute [Hamburg]
72 Uniklinik - Universitäts Klinikum Freiburg = University Medical Center Freiburg
Aurelien Dauphin
Orestis Faklaris
Sebastian Munck
  • Fonction : Auteur
Ioannis Alexopoulos
Jakob Bierwagen
  • Fonction : Auteur
Chieh-Li Chen
  • Fonction : Auteur
Ralf Dietzel
  • Fonction : Auteur
Frank Eismann
  • Fonction : Auteur
Elnaz Fazeli
  • Fonction : Auteur
Thomas Guilbert
Roland Hadleigh
  • Fonction : Auteur
Gerhard A Holst
  • Fonction : Auteur
Claudia B Jaffe
  • Fonction : Auteur
Stuart C Jarvis
  • Fonction : Auteur
Antje Keppler
  • Fonction : Auteur
Judith Lacoste
  • Fonction : Auteur
Arnaud Royon
  • Fonction : Auteur
Damir Sudar
  • Fonction : Auteur

Résumé

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, and scientific publishers; 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.

Domaines

Imagerie
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Dates et versions

hal-03120748 , version 1 (19-12-2023)

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Glyn Nelson, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, et al.. QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. 2023. ⟨hal-03120748⟩
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