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Cimini BA, Bankhead P, D'Antuono R, Fazeli E, Fernandez-Rodriguez J, Fuster-Barceló C, Haase R, Jambor HK, Jones ML, Jug F, Klemm AH, Kreshuk A, Marcotti S, Martins GG, McArdle S, Miura K, Muñoz-Barrutia A, Murphy LC, Nelson MS, Nørrelykke SF, Paul-Gilloteaux P, Pengo T, Pylvänäinen JW, Pytowski L, Ravera A, Reinke A, Rekik Y, Strambio-De-Castillia C, Thédié D, Uhlmann V, Umney O, Wiggins L, Eliceiri KW. The crucial role of bioimage analysts in scientific research and publication. J Cell Sci 2024; 137:jcs262322. [PMID: 39475207 PMCID: PMC11698046 DOI: 10.1242/jcs.262322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2024] Open
Abstract
Bioimage analysis (BIA), a crucial discipline in biological research, overcomes the limitations of subjective analysis in microscopy through the creation and application of quantitative and reproducible methods. The establishment of dedicated BIA support within academic institutions is vital to improving research quality and efficiency and can significantly advance scientific discovery. However, a lack of training resources, limited career paths and insufficient recognition of the contributions made by bioimage analysts prevent the full realization of this potential. This Perspective - the result of the recent The Company of Biologists Workshop 'Effectively Communicating Bioimage Analysis', which aimed to summarize the global BIA landscape, categorize obstacles and offer possible solutions - proposes strategies to bring about a cultural shift towards recognizing the value of BIA by standardizing tools, improving training and encouraging formal credit for contributions. We also advocate for increased funding, standardized practices and enhanced collaboration, and we conclude with a call to action for all stakeholders to join efforts in advancing BIA.
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Affiliation(s)
- Beth A. Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter Bankhead
- Edinburgh Pathology, Centre for Genomic & Experimental Medicine and CRUK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Rocco D'Antuono
- Crick Advanced Light Microscopy STP, The Francis Crick Institute, London NW1 1AT, UK
- Department of Biomedical Engineering, School of Biological Sciences, University of Reading, Reading RG6 6AY, UK
| | - Elnaz Fazeli
- Biomedicum Imaging Unit, Faculty of Medicine and HiLIFE, University of Helsinki, FI-00014 Helsinki, Finland
| | - Julia Fernandez-Rodriguez
- Centre for Cellular Imaging, Sahlgrenska Academy, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | | | - Robert Haase
- Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig, Universität Leipzig, 04105 Leipzig, Germany
| | - Helena Klara Jambor
- DAViS, University of Applied Sciences of the Grisons, 7000 Chur, Switzerland
| | - Martin L. Jones
- Electron Microscopy STP, The Francis Crick Institute, London NW1 1AT, UK
| | - Florian Jug
- Fondazione Human Technopole, 20157 Milan, Italy
| | - Anna H. Klemm
- Science for Life Laboratory BioImage Informatics Facility and Department of Information Technology, Uppsala University, SE-75105 Uppsala, Sweden
| | - Anna Kreshuk
- Cell Biology and Biophysics, European Molecular Biology Laboratory, 69115 Heidelberg, Germany
| | - Stefania Marcotti
- Randall Centre for Cell and Molecular Biophysics and Research Management & Innovation Directorate, King's College London, London SE1 1UL, UK
| | - Gabriel G. Martins
- GIMM - Gulbenkian Institute for Molecular Medicine, R. Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Sara McArdle
- La Jolla Institute for Immunology,Microscopy Core Facility, San Diego, CA 92037, USA
| | - Kota Miura
- Bioimage Analysis & Research, BIO-Plaza 1062, Nishi-Furumatsu 2-26-22 Kita-ku, Okayama, 700-0927, Japan
| | | | - Laura C. Murphy
- Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Michael S. Nelson
- University of Wisconsin-Madison,Biomedical Engineering, Madison, WI 53706, USA
| | | | | | - Thomas Pengo
- Minnesota Supercomputing Institute,University of Minnesota Twin Cities, Minneapolis, MN 55005, USA
| | - Joanna W. Pylvänäinen
- Åbo Akademi University, Faculty of Science and Engineering, Biosciences, 20520 Turku, Finland
| | - Lior Pytowski
- Pixel Biology Ltd, 9 South Park Court, East Avenue, Oxford OX4 1YZ, UK
| | - Arianna Ravera
- Scientific Computing and Research Support Unit, University of Lausanne, 1005 Lausanne, Switzerland
| | - Annika Reinke
- Division of Intelligent Medical Systems and Helmholtz Imaging, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Yousr Rekik
- Université Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de chimie et de biologie des métaux, F-38000 Grenoble, France
- Université Grenoble Alpes, CEA, IRIG, Laboratoire Modélisation et Exploration des Matériaux, F-38000 Grenoble, France
| | | | - Daniel Thédié
- Institute of Cell Biology, The University of Edinburgh, Edinburgh EH9 3FF, UK
| | | | - Oliver Umney
- School of Computing, University of Leeds, Leeds LS2 9JT, UK
| | - Laura Wiggins
- University of Sheffield, Department of Materials Science and Engineering, Sheffield S10 2TN, UK
| | - Kevin W. Eliceiri
- University of Wisconsin-Madison,Biomedical Engineering, Madison, WI 53706, USA
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2
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Cimini BA, Tromans-Coia C, Stirling DR, Sivagurunathan S, Senft RA, Ryder PV, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz M, Weisbart E, Carpenter AE. A postdoctoral training program in bioimage analysis. Mol Biol Cell 2024; 35:pe2. [PMID: 39105698 PMCID: PMC11449385 DOI: 10.1091/mbc.e24-05-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/25/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
We herein describe a postdoctoral training program designed to train biologists with microscopy experience in bioimage analysis. We detail the rationale behind the program, the various components of the training program, and outcomes in terms of works produced and the career effects on past participants. We analyze the results of an anonymous survey distributed to past and present participants, indicating overall high value of all 12 rated aspects of the program, but significant heterogeneity in which aspects were most important to each participant. Finally, we propose this model as a template for other programs which may want to train experts in professional skill sets, and discuss the important considerations when running such a program. We believe that such programs can have extremely positive impact for both the trainees themselves and the broader scientific community.
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Affiliation(s)
| | | | | | | | | | | | | | - Paula Llanos
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Nasim Jamali
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | | | - Mario Cruz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Erin Weisbart
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
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3
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Renaud O, Aulner N, Salles A, Halidi N, Brunstein M, Mallet A, Aumayr K, Terjung S, Levy D, Lippens S, Verbavatz JM, Heuser T, Santarella-Mellwig R, Tinevez JY, Woller T, Botzki A, Cawthorne C, Munck S. Staying on track - Keeping things running in a high-end scientific imaging core facility. J Microsc 2024; 294:276-294. [PMID: 38656474 DOI: 10.1111/jmi.13304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Modern life science research is a collaborative effort. Few research groups can single-handedly support the necessary equipment, expertise and personnel needed for the ever-expanding portfolio of technologies that are required across multiple disciplines in today's life science endeavours. Thus, research institutes are increasingly setting up scientific core facilities to provide access and specialised support for cutting-edge technologies. Maintaining the momentum needed to carry out leading research while ensuring high-quality daily operations is an ongoing challenge, regardless of the resources allocated to establish such facilities. Here, we outline and discuss the range of activities required to keep things running once a scientific imaging core facility has been established. These include managing a wide range of equipment and users, handling repairs and service contracts, planning for equipment upgrades, renewals, or decommissioning, and continuously upskilling while balancing innovation and consolidation.
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Affiliation(s)
- Oliver Renaud
- Cell and Tissue Imaging Platform (PICT-IBiSA, France-BioImaging), Institut Curie, Université PSL, Sorbonne Université, CNRS, Inserm, Paris, France
| | - Nathalie Aulner
- Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Paris, France
| | - Audrey Salles
- Centre de Ressources et Recherches Technologiques (UTechS-PBI, C2RT), Institut Pasteur, Université Paris Cité, Photonic Bio-Imaging, Paris, France
| | - Nadia Halidi
- Advanced Light Microscopy Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maia Brunstein
- Bioimaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, Paris, France
| | - Adeline Mallet
- Centre de Ressources et Recherches Technologiques (UBI, C2RT), Institut Pasteur, Université Paris Cité, Ultrastructural BioImaging, Paris, France
| | - Karin Aumayr
- BioOptics Facility, Research Institute of Molecular Pathology (IMP) Campus-Vienna-Biocenter 1, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohr-Gasse 3, Vienna, Austria
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences (GMI), Dr. Bohr-Gasse 3, Vienna, Austria
| | - Stefan Terjung
- Advanced Light Microscopy Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Daniel Levy
- Cell and Tissue Imaging Platform (PICT-IBiSA, France-BioImaging), Institut Curie, Université PSL, Sorbonne Université, CNRS, Inserm, Paris, France
| | | | - Jean-Marc Verbavatz
- Institut Jacques Monod (Imagoseine), Université Paris Cité, CNRS, Paris, France
| | - Thomas Heuser
- Vienna Biocenter Core Facilities GmbH (VBCF), Wien, Austria
| | | | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Tatiana Woller
- VIB Technology Training, Data Core, VIB BioImaging Core, VIB, Ghent, Belgium
- Neuroscience Department, KU Leuven, Leuven, Belgium
| | | | - Christopher Cawthorne
- Department of Imaging and Pathology, Nuclear Medicine and Molecular Imaging, KU Leuven, Leuven, Belgium
| | - Sebastian Munck
- Neuroscience Department, KU Leuven, Leuven, Belgium
- VIB BioImaging Core, VIB, Leuven, Belgium
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4
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Tranfield EM, Lippens S. Future proofing core facilities with a seven-pillar model. J Microsc 2024; 294:411-419. [PMID: 38700841 DOI: 10.1111/jmi.13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 05/21/2024]
Abstract
Centralised core facilities have evolved into vital components of life science research, transitioning from a primary focus on centralising equipment to ensuring access to technology experts across all facets of an experimental workflow. Herein, we put forward a seven-pillar model to define what a core facility needs to meet its overarching goal of facilitating research. The seven equally weighted pillars are Technology, Core Facility Team, Training, Career Tracks, Technical Support, Community and Transparency. These seven pillars stand on a solid foundation of cultural, operational and framework policies including the elements of transparent and stable funding strategies, modern human resources support, progressive facility leadership and management as well as clear institute strategies and policies. This foundation, among other things, ensures a tight alignment of the core facilities to the vision and mission of the institute. To future-proof core facilities, it is crucial to foster all seven of these pillars, particularly focusing on newly identified pillars such as career tracks, thus enabling core facilities to continue supporting research and catalysing scientific advancement. Lay abstract: In research, there is a growing trend to bring advanced, high-performance equipment together into a centralised location. This is done to streamline how the equipment purchase is financed, how the equipment is maintained, and to enable an easier approach for research scientists to access these tools in a location that is supported by a team of technology experts who can help scientists use the equipment. These centralised equipment centres are called Core Facilities. The core facility model is relatively new in science and it requires an adapted approach to how core facilities are built and managed. In this paper, we put forward a seven-pillar model of the important supporting elements of core facilities. These supporting elements are: Technology (the instruments themselves), Core Facility Team (the technology experts who operate the instruments), Training (of the staff and research community), Career Tracks (for the core facility staff), Technical Support (the process of providing help to apply the technology to a scientific question), Community (of research scientist, technology experts and developers) and Transparency (of how the core facility works and the costs associated with using the service). These pillars stand on the bigger foundation of clear policies, guidelines, and leadership approaches at the institutional level. With a focus on these elements, the authors feel core facilities will be well positioned to support scientific discovery in the future.
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Affiliation(s)
- Erin M Tranfield
- VIB Bioimaging Core Ghent, VIB, Zwijnaarde, Belgium
- VIB Center for Inflammation Research, Ghent University, Zwijnaarde, Belgium
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5
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Soltwedel JR, Haase R. Challenges and opportunities for bioimage analysis core-facilities. J Microsc 2024; 294:338-349. [PMID: 37199456 DOI: 10.1111/jmi.13192] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 05/19/2023]
Abstract
Recent advances in microscopy imaging and image analysis motivate more and more institutes worldwide to establish dedicated core-facilities for bioimage analysis. To maximise the benefits research groups at these institutes gain from their core-facilities, they should be established to fit well into their respective environment. In this article, we introduce common collaborator requests and corresponding potential services core-facilities can offer. We also discuss potential competing interests between the targeted missions and implementations of services to guide decision makers and core-facility founders to circumvent common pitfalls.
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Affiliation(s)
| | - Robert Haase
- DFG Cluster of Excellence 'Physics of Life', TU Dresden, Germany
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6
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Cimini BA, Tromans-Coia C, Stirling D, Sivagurunathan S, Senft R, Ryder P, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz M, Weisbart E, Carpenter AE. A Postdoctoral Training Program in Bioimage Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593910. [PMID: 38798545 PMCID: PMC11118354 DOI: 10.1101/2024.05.13.593910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
We herein describe a postdoctoral training program designed to train biologists with microscopy experience in bioimage analysis. We detail the rationale behind the program, the various components of the training program, and outcomes in terms of works produced and the career effects on past participants. We analyze the results of an anonymous survey distributed to past and present participants, indicating overall high value of all 12 rated aspects of the program, but significant heterogeneity in which aspects were most important to each participant. Finally, we propose this model as a template for other programs which may want to train experts in professional skill sets, and discuss the important considerations when running such a program. We believe that such programs can have extremely positive impact for both the trainees themselves and the broader scientific community.
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Affiliation(s)
- Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | | | - David Stirling
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | | | - Rebecca Senft
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Pearl Ryder
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Esteban Miglietta
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Paula Llanos
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Nasim Jamali
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | | | | | - Mario Cruz
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Erin Weisbart
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge MA, USA
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