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Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho MT, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Le Dévédec S, Le Guyader S, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK. Community-developed checklists for publishing images and image analyses. Nat Methods 2024; 21:170-181. [PMID: 37710020 PMCID: PMC10922596 DOI: 10.1038/s41592-023-01987-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/26/2023] [Indexed: 09/16/2023]
Abstract
Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However, for scientists wishing to publish obtained images and image-analysis results, there are currently no unified guidelines for best practices. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here, we present community-developed checklists for preparing light microscopy images and describing image analyses for publications. These checklists offer authors, readers and publishers key recommendations for image formatting and annotation, color selection, data availability and reporting image-analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby to heighten the quality and explanatory power of microscopy data.
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Affiliation(s)
- Christopher Schmied
- Fondazione Human Technopole, Milano, Italy.
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Michael S Nelson
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Sergiy Avilov
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gert-Jan Bakker
- Medical BioSciences Department, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Cristina Bertocchi
- Laboratory for Molecular Mechanics of Cell Adhesions, Pontificia Universidad Católica de Chile Santiago, Santiago de Chile, Chile
- Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | | | | | - Jan Brocher
- Scientific Image Processing and Analysis, BioVoxxel, Ludwigshafen, Germany
| | - Mariana T Carvalho
- Nanophotonics and BioImaging Facility at INL, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | | | - Jana Christopher
- Biochemistry Center Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Beth A Cimini
- Imaging Platform, Broad Institute, Cambridge, MA, USA
| | - Eduardo Conde-Sousa
- i3S, Instituto de Investigação e Inovação Em Saúde and INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Michael Ebner
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Rupert Ecker
- Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- TissueGnostics GmbH, Vienna, Austria
| | - Kevin Eliceiri
- Department of Medical Physics and Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Julia Fernandez-Rodriguez
- Centre for Cellular Imaging Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Nadia Halidi
- Advanced Light Microscopy Unit, Centre for Genomic Regulation, Barcelona, Spain
| | - Mathias Hammer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Matthew Hartley
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Hinxton, UK
| | - Marie Held
- Centre for Cell Imaging, the University of Liverpool, Liverpool, UK
| | | | - Varun Kapoor
- Department of AI Research, Kapoor Labs, Paris, France
| | | | | | - Sylvia Le Dévédec
- Division of Drug Discovery and Safety, Cell Observatory, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | | | - Penghuan Liu
- Key Laboratory for Modern Measurement Technology and Instruments of Zhejiang Province, College of Optical and Electronic Technology, China Jiliang University, Hangzhou, China
| | - Gabriel G Martins
- Advanced Imaging Facility, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Kota Miura
- Bioimage Analysis and Research, Heidelberg, Germany
| | | | - Roland Nitschke
- Life Imaging Center, Signalling Research Centres CIBSS and BIOSS, University of Freiburg, Freiburg, Germany
| | - Alison North
- Bio-Imaging Resource Center, the Rockefeller University, New York, NY, USA
| | - Adam C Parslow
- Baker Institute Microscopy Platform, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Alex Payne-Dwyer
- School of Physics, Engineering and Technology, University of York, Heslington, UK
| | - Laure Plantard
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Rizwan Ali
- King Abdullah International Medical Research Center (KAIMRC), Medical Research Core Facility and Platforms (MRCFP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Britta Schroth-Diez
- Light Microscopy Facility, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Dresden, Germany
| | | | - Ryan T Scott
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Arne Seitz
- BioImaging and Optics Platform, Faculty of Life Sciences (SV), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Olaf Selchow
- Microscopy and BioImaging Consulting, Image Processing and Large Data Handling, Gera, Germany
| | - Ved P Sharma
- Bio-Imaging Resource Center, the Rockefeller University, New York, NY, USA
| | | | - Sathya Srinivasan
- Imaging and Morphology Support Core, Oregon National Primate Research Center, OHSU West Campus, Beaverton, OR, USA
| | | | - Douglas Taatjes
- Department of Pathology and Laboratory Medicine, Microscopy Imaging Center, Center for Biomedical Shared Resources, University of Vermont, Burlington, VT, USA
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Greco SH, Davis CH, Hicks CW, Kaye AE, Maxwell JE, Salles A, Henry MC. How to Review a Surgical Scientific Paper: A Guide for Critical Appraisal. ANNALS OF SURGERY OPEN 2021; 2:e027. [PMID: 37638253 PMCID: PMC10455126 DOI: 10.1097/as9.0000000000000027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/01/2020] [Indexed: 11/26/2022] Open
Abstract
It is important for surgeons to participate in the peer-review process of scientific literature. As the number of published manuscripts continues to increase, there is a great need for volunteerism in this arena. However, there is little formal or informal training, which can help surgeons provide unbiased and meaningful reviews. Therefore, it is critical to provide more resources and guidelines to aid surgeons during the review process. The purpose of this paper is to provide a structured guide for a quality review of a surgical paper. This review represents the work of the Association of Women Surgeons Publications Committee.
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Affiliation(s)
- Stephanie H. Greco
- From the Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA
| | | | - Caitlin W. Hicks
- Department of Surgery, Division of Vascular and Endovascular Therapy, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alison E. Kaye
- Division of Plastic Surgery, Children’s Mercy Kansas City, Kansas City, MO
| | - Jessica E. Maxwell
- Department of Surgery, Division of Surgical Oncology, University of Nebraska Medical Center, Omaha, NE
| | - Arghavan Salles
- Scholar in Residence, Stanford University School of Medicine, Stanford, CA
| | - Marion C.W. Henry
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ
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Bik EM, Fang FC, Kullas AL, Davis RJ, Casadevall A. Analysis and Correction of Inappropriate Image Duplication: the Molecular and Cellular Biology Experience. Mol Cell Biol 2018; 38:e00309-18. [PMID: 30037982 PMCID: PMC6168979 DOI: 10.1128/mcb.00309-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/11/2018] [Accepted: 07/17/2018] [Indexed: 01/25/2023] Open
Abstract
We analyzed 960 papers published in Molecular and Cellular Biology (MCB) from 2009 to 2016 and found 59 (6.1%) to contain inappropriately duplicated images. The 59 instances of inappropriate image duplication led to 41 corrections, 5 retractions, and 13 instances in which no action was taken. Our experience suggests that the majority of inappropriate image duplications result from errors during figure preparation that can be remedied by correction. Nevertheless, ∼10% of papers with inappropriate image duplications in MCB were retracted (∼0.5% of total). If this proportion is representative, then as many as 35,000 papers in the literature are candidates for retraction due to inappropriate image duplication. The resolution of inappropriate image duplication concerns after publication required an average of 6 h of journal staff time per published paper. MCB instituted a pilot program to screen images of accepted papers prior to publication that identified 12 manuscripts (14.5% out of 83) with image concerns in 2 months. The screening and correction of papers before publication required an average of 30 min of staff time per problematic paper. Image screening can identify papers with problematic images prior to publication, reduces postpublication problems, and requires less staff time than the correction of problems after publication.
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Affiliation(s)
| | - Ferric C Fang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Amy L Kullas
- Journals Department, American Society for Microbiology (ASM), Washington, DC, USA
| | - Roger J Davis
- Howard Hughes Medical Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
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Heinrich M, Lardos A, Leonti M, Weckerle C, Willcox M, Applequist W, Ladio A, Lin Long C, Mukherjee P, Stafford G. Best practice in research: Consensus Statement on Ethnopharmacological Field Studies - ConSEFS. JOURNAL OF ETHNOPHARMACOLOGY 2018; 211:329-339. [PMID: 28818646 DOI: 10.1016/j.jep.2017.08.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/27/2017] [Accepted: 08/09/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Ethnopharmacological research aims at gathering information on local and traditional uses of plants and other natural substances. However, the approaches used and the methods employed vary, and while such a variability is desirable in terms of scientific diversity, research must adhere to well defined quality standards and reproducible methods OBJECTIVES: With ConSEFS (the Consensus Statement on Ethnopharmacological Field Studies) we want to define best-practice in developing, conducting and reporting field studies focusing on local and traditional uses of medicinal and food plants, including studies using a historical approach. METHODS After first developing an initial draft the core group invited community-wide feedback from researchers both through a web-based consultation and a series of workshops at conferences during 2017. OUTCOMES The consultation resulted in a large number of responses. Feedback was received via a weblink on the Journal of Ethnopharmacology's website (ca. 100 responses), other oral and written responses (ca. 50) and discussions with stakeholders at four conferences. The main outcome is a checklist, covering best practice for designing, implementing and recording ethnopharmacological field studies and historical studies. CONCLUSIONS Prior to starting ethnopharmacological field research, it is essential that the authors are fully aware of the best practice in the field. For the first time in the field of ethnopharmacology a community-wide document defines guidelines for best practice on how to conduct and report such studies. It will need to be updated and further developed. While the feedback has been based on responses by many experienced researchers, there is a need to test it in practice by using it both in implementing and reporting field studies (or historical studies), and peer-review.
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Affiliation(s)
- Michael Heinrich
- Research Cluster 'Biodiversity and Medicines'/Research Group 'Pharmacognosy and Phytotherapy', UCL School of Pharmacy, University in London, 29-39 Brunswick Sq., London WC1N 1AX, UK.
| | | | - Marco Leonti
- Department of Biomedical Sciences, University of Cagliari, Via Ospedale 72, 09124 Cagliari (CA), Italy.
| | - Caroline Weckerle
- Institute of Systematic Botany, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland.
| | - Merlin Willcox
- Department of Primary Care and Population Sciences, University of Southampton, UK.
| | - Wendy Applequist
- Missouri Botanical Garden, P.O. Box 299, St. Louis, MO 63166-0299, USA.
| | - Ana Ladio
- Laboratorio Ecotono, INIBIOMA, CONICET-Universidad Nacional del Comahue, Argentina.
| | - Chun Lin Long
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Pulok Mukherjee
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India.
| | - Gary Stafford
- Department of Botany and Zoology, Stellenbosch University, 7601 Stellenbosch, South Africa.
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