1
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Sneider A, Liu Y, Starich B, Du W, Nair PR, Marar C, Faqih N, Ciotti GE, Kim JH, Krishnan S, Ibrahim S, Igboko M, Locke A, Lewis DM, Hong H, Karl MN, Vij R, Russo GC, Gómez-de-Mariscal E, Habibi M, Muñoz-Barrutia A, Gu L, Eisinger-Mathason TSK, Wirtz D. Small extracellular vesicles promote stiffness-mediated metastasis. Cancer Res Commun 2024:743072. [PMID: 38630893 DOI: 10.1158/2767-9764.crc-23-0431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/13/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Tissue stiffness is a critical prognostic factor in breast cancer and is associated with metastatic progression. Here we show an alternative and complementary hypothesis of tumor progression whereby physiological matrix stiffness affects the quantity and protein cargo of small EVs produced by cancer cells, which in turn aid cancer cell dissemination. Primary patient breast tissue produces significantly more EVs from stiff tumor tissue than soft tumor adjacent tissue. EVs released by cancer cells on matrices that model human breast tumors (25 kPa; stiff EVs) feature increased adhesion molecule presentation (ITGα2β1, ITGα6β4, ITGα6β1, CD44) compared to EVs from softer normal tissue (0.5 kPa; soft EVs), which facilitates their binding to extracellular matrix (ECM) proteins including collagen IV, and a 3-fold increase in homing ability to distant organs in mice. In a zebrafish xenograft model, stiff EVs aid cancer cell dissemination. Moreover, normal, resident lung fibroblasts treated with stiff and soft EVs change their gene expression profiles to adopt a cancer associated fibroblast (CAF) phenotype. These findings show that EV quantity, cargo, and function depend heavily on the mechanical properties of the extracellular microenvironment.
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Affiliation(s)
| | - Ying Liu
- University of Pennsylvania, Philadelphia, United States
| | | | | | | | | | | | | | - Joo Ho Kim
- Johns Hopkins University, Baltimore, MD, United States
| | | | | | | | | | | | | | | | | | | | | | - Mehran Habibi
- Johns Hopkins University, Baltimore, MD, United States
| | | | - Luo Gu
- Johns Hopkins University, Baltimore, MD, United States
| | | | - Denis Wirtz
- Johns Hopkins University, Baltimore, United States
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2
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Sneider A, Liu Y, Starich B, Du W, Marar C, Faqih N, Ciotti GE, Kim JH, Krishnan S, Ibrahim S, Igboko M, Locke A, Lewis DM, Hong H, Karl M, Vij R, Russo GC, Nair P, Gómez-de-Mariscal E, Habibi M, Muñoz-Barrutia A, Gu L, Eisinger-Mathason TSK, Wirtz D. Small extracellular vesicles promote stiffness-mediated metastasis. bioRxiv 2024:2023.07.01.545937. [PMID: 37425743 PMCID: PMC10327142 DOI: 10.1101/2023.07.01.545937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Tissue stiffness is a critical prognostic factor in breast cancer and is associated with metastatic progression. Here we show an alternative and complementary hypothesis of tumor progression whereby physiological matrix stiffness affects the quantity and protein cargo of small EVs produced by cancer cells, which in turn drive their metastasis. Primary patient breast tissue produces significantly more EVs from stiff tumor tissue than soft tumor adjacent tissue. EVs released by cancer cells on matrices that model human breast tumors (25 kPa; stiff EVs) feature increased adhesion molecule presentation (ITGα 2 β 1 , ITGα 6 β 4 , ITGα 6 β 1 , CD44) compared to EVs from softer normal tissue (0.5 kPa; soft EVs), which facilitates their binding to extracellular matrix (ECM) protein collagen IV, and a 3-fold increase in homing ability to distant organs in mice. In a zebrafish xenograft model, stiff EVs aid cancer cell dissemination through enhanced chemotaxis. Moreover, normal, resident lung fibroblasts treated with stiff and soft EVs change their gene expression profiles to adopt a cancer associated fibroblast (CAF) phenotype. These findings show that EV quantity, cargo, and function depend heavily on the mechanical properties of the extracellular microenvironment.
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3
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Nair PR, Danilova L, Gómez-de-Mariscal E, Kim D, Fan R, Muñoz-Barrutia A, Fertig EJ, Wirtz D. MLL1 regulates cytokine-driven cell migration and metastasis. Sci Adv 2024; 10:eadk0785. [PMID: 38478601 PMCID: PMC10936879 DOI: 10.1126/sciadv.adk0785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/07/2024] [Indexed: 03/17/2024]
Abstract
Cell migration is a critical contributor to metastasis. Cytokine production and its role in cancer cell migration have been traditionally associated with immune cells. We find that the histone methyltransferase Mixed-Lineage Leukemia 1 (MLL1) controls 3D cell migration via cytokines, IL-6, IL-8, and TGF-β1, secreted by the cancer cells themselves. MLL1, with its scaffold protein Menin, controls actin filament assembly via the IL-6/8/pSTAT3/Arp3 axis and myosin contractility via the TGF-β1/Gli2/ROCK1/2/pMLC2 axis, which together regulate dynamic protrusion generation and 3D cell migration. MLL1 also regulates cell proliferation via mitosis-based and cell cycle-related pathways. Mice bearing orthotopic MLL1-depleted tumors exhibit decreased lung metastatic burden and longer survival. MLL1 depletion leads to lower metastatic burden even when controlling for the difference in primary tumor growth rates. Combining MLL1-Menin inhibitor with paclitaxel abrogates tumor growth and metastasis, including preexistent metastasis. These results establish MLL1 as a potent regulator of cell migration and highlight the potential of targeting MLL1 in patients with metastatic disease.
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Affiliation(s)
- Praful R. Nair
- Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ludmila Danilova
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Estibaliz Gómez-de-Mariscal
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid, 28911 Leganés, and Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- Optical Cell Biology Group, Instituto Gulbenkian de Ciência, R. Q.ta Grande 6 2780, 2780-156 Oeiras, Portugal
| | - Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Arrate Muñoz-Barrutia
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid, 28911 Leganés, and Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Elana J. Fertig
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Denis Wirtz
- Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins Physical Sciences-Oncology Center, The Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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4
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Morgado L, Gómez-de-Mariscal E, Heil HS, Henriques R. The rise of data-driven microscopy powered by machine learning. J Microsc 2024. [PMID: 38445705 DOI: 10.1111/jmi.13282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Optical microscopy is an indispensable tool in life sciences research, but conventional techniques require compromises between imaging parameters like speed, resolution, field of view and phototoxicity. To overcome these limitations, data-driven microscopes incorporate feedback loops between data acquisition and analysis. This review overviews how machine learning enables automated image analysis to optimise microscopy in real time. We first introduce key data-driven microscopy concepts and machine learning methods relevant to microscopy image analysis. Subsequently, we highlight pioneering works and recent advances in integrating machine learning into microscopy acquisition workflows, including optimising illumination, switching modalities and acquisition rates, and triggering targeted experiments. We then discuss the remaining challenges and future outlook. Overall, intelligent microscopes that can sense, analyse and adapt promise to transform optical imaging by opening new experimental possibilities.
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Affiliation(s)
- Leonor Morgado
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Abbelight, Cachan, France
| | | | - Hannah S Heil
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Ricardo Henriques
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
- UCL-Laboratory for Molecular Cell Biology, University College London, London, UK
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5
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Gómez-de-Mariscal E, Del Rosario M, Pylvänäinen JW, Jacquemet G, Henriques R. Harnessing artificial intelligence to reduce phototoxicity in live imaging. J Cell Sci 2024; 137:jcs261545. [PMID: 38324353 PMCID: PMC10912813 DOI: 10.1242/jcs.261545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
Fluorescence microscopy is essential for studying living cells, tissues and organisms. However, the fluorescent light that switches on fluorescent molecules also harms the samples, jeopardizing the validity of results - particularly in techniques such as super-resolution microscopy, which demands extended illumination. Artificial intelligence (AI)-enabled software capable of denoising, image restoration, temporal interpolation or cross-modal style transfer has great potential to rescue live imaging data and limit photodamage. Yet we believe the focus should be on maintaining light-induced damage at levels that preserve natural cell behaviour. In this Opinion piece, we argue that a shift in role for AIs is needed - AI should be used to extract rich insights from gentle imaging rather than recover compromised data from harsh illumination. Although AI can enhance imaging, our ultimate goal should be to uncover biological truths, not just retrieve data. It is essential to prioritize minimizing photodamage over merely pushing technical limits. Our approach is aimed towards gentle acquisition and observation of undisturbed living systems, aligning with the essence of live-cell fluorescence microscopy.
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Affiliation(s)
| | | | - Joanna W. Pylvänäinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku 20500, Finland
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku 20500, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku 20100, Finland
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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6
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García López de Haro C, Dallongeville S, Musset T, Gómez-de-Mariscal E, Sage D, Ouyang W, Muñoz-Barrutia A, Tinevez JY, Olivo-Marin JC. JDLL: a library to run deep learning models on Java bioimage informatics platforms. Nat Methods 2024; 21:7-8. [PMID: 38191929 DOI: 10.1038/s41592-023-02129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Affiliation(s)
| | - Stéphane Dallongeville
- Bioimage Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France
- CNRS UMR 3691, Institut Pasteur, Paris, France
| | - Thomas Musset
- Bioimage Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France
- CNRS UMR 3691, Institut Pasteur, Paris, France
| | | | - Daniel Sage
- Biomedical Imaging Group and Center for Imaging, Ecole Polytechnique de Lausanne (EPFL), Lausanne, Switzerland
| | - Wei Ouyang
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Arrate Muñoz-Barrutia
- Biomedical Sciences and Engineering Laboratory, Universidad Carlos III de Madrid, Leganés, Spain
| | - Jean-Yves Tinevez
- Image Analysis Hub, Institut Pasteur, Université Paris Cité, Paris, France.
| | - Jean-Christophe Olivo-Marin
- Bioimage Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France.
- CNRS UMR 3691, Institut Pasteur, Paris, France.
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7
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Pylvänäinen JW, Gómez-de-Mariscal E, Henriques R, Jacquemet G. Live-cell imaging in the deep learning era. Curr Opin Cell Biol 2023; 85:102271. [PMID: 37897927 DOI: 10.1016/j.ceb.2023.102271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/30/2023]
Abstract
Live imaging is a powerful tool, enabling scientists to observe living organisms in real time. In particular, when combined with fluorescence microscopy, live imaging allows the monitoring of cellular components with high sensitivity and specificity. Yet, due to critical challenges (i.e., drift, phototoxicity, dataset size), implementing live imaging and analyzing the resulting datasets is rarely straightforward. Over the past years, the development of bioimage analysis tools, including deep learning, is changing how we perform live imaging. Here we briefly cover important computational methods aiding live imaging and carrying out key tasks such as drift correction, denoising, super-resolution imaging, artificial labeling, tracking, and time series analysis. We also cover recent advances in self-driving microscopy.
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Affiliation(s)
- Joanna W Pylvänäinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi, University, 20520 Turku, Finland
| | | | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras 2780-156, Portugal; University College London, London WC1E 6BT, United Kingdom
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi, University, 20520 Turku, Finland; Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland; InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Turku Bioimaging, University of Turku and Åbo Akademi University, FI- 20520 Turku, Finland.
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8
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Maška M, Ulman V, Delgado-Rodriguez P, Gómez-de-Mariscal E, Nečasová T, Guerrero Peña FA, Ren TI, Meyerowitz EM, Scherr T, Löffler K, Mikut R, Guo T, Wang Y, Allebach JP, Bao R, Al-Shakarji NM, Rahmon G, Toubal IE, Palaniappan K, Lux F, Matula P, Sugawara K, Magnusson KEG, Aho L, Cohen AR, Arbelle A, Ben-Haim T, Raviv TR, Isensee F, Jäger PF, Maier-Hein KH, Zhu Y, Ederra C, Urbiola A, Meijering E, Cunha A, Muñoz-Barrutia A, Kozubek M, Ortiz-de-Solórzano C. The Cell Tracking Challenge: 10 years of objective benchmarking. Nat Methods 2023:10.1038/s41592-023-01879-y. [PMID: 37202537 PMCID: PMC10333123 DOI: 10.1038/s41592-023-01879-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 04/13/2023] [Indexed: 05/20/2023]
Abstract
The Cell Tracking Challenge is an ongoing benchmarking initiative that has become a reference in cell segmentation and tracking algorithm development. Here, we present a significant number of improvements introduced in the challenge since our 2017 report. These include the creation of a new segmentation-only benchmark, the enrichment of the dataset repository with new datasets that increase its diversity and complexity, and the creation of a silver standard reference corpus based on the most competitive results, which will be of particular interest for data-hungry deep learning-based strategies. Furthermore, we present the up-to-date cell segmentation and tracking leaderboards, an in-depth analysis of the relationship between the performance of the state-of-the-art methods and the properties of the datasets and annotations, and two novel, insightful studies about the generalizability and the reusability of top-performing methods. These studies provide critical practical conclusions for both developers and users of traditional and machine learning-based cell segmentation and tracking algorithms.
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Affiliation(s)
- Martin Maška
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Vladimír Ulman
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
- IT4Innovations National Supercomputing Center, VSB - Technical University of Ostrava, Ostrava, Czech Republic
| | - Pablo Delgado-Rodriguez
- Bioengineering Department, Universidad Carlos III de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Estibaliz Gómez-de-Mariscal
- Bioengineering Department, Universidad Carlos III de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Optical Cell Biology, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Tereza Nečasová
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Fidel A Guerrero Peña
- Centro de Informatica, Universidade Federal de Pernambuco, Recife, Brazil
- Center for Advanced Methods in Biological Image Analysis, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Tsang Ing Ren
- Centro de Informatica, Universidade Federal de Pernambuco, Recife, Brazil
| | - Elliot M Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Tim Scherr
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Katharina Löffler
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Ralf Mikut
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Tianqi Guo
- The Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
| | - Yin Wang
- The Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
| | - Jan P Allebach
- The Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
| | - Rina Bao
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- CIVA Lab, Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Noor M Al-Shakarji
- CIVA Lab, Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Gani Rahmon
- CIVA Lab, Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Imad Eddine Toubal
- CIVA Lab, Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Kannappan Palaniappan
- CIVA Lab, Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Filip Lux
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Petr Matula
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Ko Sugawara
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Paris, France
| | | | - Layton Aho
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA
| | - Andrew R Cohen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA
| | - Assaf Arbelle
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Tal Ben-Haim
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Tammy Riklin Raviv
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Fabian Isensee
- Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz Imaging, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul F Jäger
- Helmholtz Imaging, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Interactive Machine Learning Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Klaus H Maier-Hein
- Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Pattern Analysis and Learning Group, Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Yanming Zhu
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
- Griffith University, Nathan, Queensland, Australia
| | - Cristina Ederra
- Biomedical Engineering Program and Ciberonc, Center for Applied Medical Research, Universidad de Navarra, Pamplona, Spain
| | - Ainhoa Urbiola
- Biomedical Engineering Program and Ciberonc, Center for Applied Medical Research, Universidad de Navarra, Pamplona, Spain
| | - Erik Meijering
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Alexandre Cunha
- Center for Advanced Methods in Biological Image Analysis, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Arrate Muñoz-Barrutia
- Bioengineering Department, Universidad Carlos III de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Michal Kozubek
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic.
| | - Carlos Ortiz-de-Solórzano
- Biomedical Engineering Program and Ciberonc, Center for Applied Medical Research, Universidad de Navarra, Pamplona, Spain.
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9
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Volpe G, Wählby C, Tian L, Hecht M, Yakimovich A, Monakhova K, Waller L, Sbalzarini IF, Metzler CA, Xie M, Zhang K, Lenton ICD, Rubinsztein-Dunlop H, Brunner D, Bai B, Ozcan A, Midtvedt D, Wang H, Sladoje N, Lindblad J, Smith JT, Ochoa M, Barroso M, Intes X, Qiu T, Yu LY, You S, Liu Y, Ziatdinov MA, Kalinin SV, Sheridan A, Manor U, Nehme E, Goldenberg O, Shechtman Y, Moberg HK, Langhammer C, Špačková B, Helgadottir S, Midtvedt B, Argun A, Thalheim T, Cichos F, Bo S, Hubatsch L, Pineda J, Manzo C, Bachimanchi H, Selander E, Homs-Corbera A, Fränzl M, de Haan K, Rivenson Y, Korczak Z, Adiels CB, Mijalkov M, Veréb D, Chang YW, Pereira JB, Matuszewski D, Kylberg G, Sintorn IM, Caicedo JC, Cimini BA, Bell MAL, Saraiva BM, Jacquemet G, Henriques R, Ouyang W, Le T, Gómez-de-Mariscal E, Sage D, Muñoz-Barrutia A, Lindqvist EJ, Bergman J. Roadmap on Deep Learning for Microscopy. ArXiv 2023:2303.03793. [PMID: 36945686 PMCID: PMC10029045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.
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10
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Spahn C, Gómez-de-Mariscal E, Laine RF, Pereira PM, von Chamier L, Conduit M, Pinho MG, Jacquemet G, Holden S, Heilemann M, Henriques R. DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches. Commun Biol 2022; 5:688. [PMID: 35810255 PMCID: PMC9271087 DOI: 10.1038/s42003-022-03634-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/23/2022] [Indexed: 11/09/2022] Open
Abstract
This work demonstrates and guides how to use a range of state-of-the-art artificial neural-networks to analyse bacterial microscopy images using the recently developed ZeroCostDL4Mic platform. We generated a database of image datasets used to train networks for various image analysis tasks and present strategies for data acquisition and curation, as well as model training. We showcase different deep learning (DL) approaches for segmenting bright field and fluorescence images of different bacterial species, use object detection to classify different growth stages in time-lapse imaging data, and carry out DL-assisted phenotypic profiling of antibiotic-treated cells. To also demonstrate the ability of DL to enhance low-phototoxicity live-cell microscopy, we showcase how image denoising can allow researchers to attain high-fidelity data in faster and longer imaging. Finally, artificial labelling of cell membranes and predictions of super-resolution images allow for accurate mapping of cell shape and intracellular targets. Our purposefully-built database of training and testing data aids in novice users' training, enabling them to quickly explore how to analyse their data through DL. We hope this lays a fertile ground for the efficient application of DL in microbiology and fosters the creation of tools for bacterial cell biology and antibiotic research.
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Affiliation(s)
- Christoph Spahn
- Department of Natural Products in Organismic Interaction, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.
| | | | - Romain F Laine
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
- Micrographia Bio, Translation and Innovation hub 84 Wood lane, W120BZ, London, UK
| | - Pedro M Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lucas von Chamier
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Mia Conduit
- Centre for Bacterial Cell Biology, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, NE24AX, United Kingdom
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland
| | - Séamus Holden
- Centre for Bacterial Cell Biology, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, NE24AX, United Kingdom
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Frankfurt, Germany.
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal.
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK.
- The Francis Crick Institute, London, UK.
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Gómez-de-Mariscal E, García-López-de-Haro C, Ouyang W, Donati L, Lundberg E, Unser M, Muñoz-Barrutia A, Sage D. DeepImageJ: A user-friendly environment to run deep learning models in ImageJ. Nat Methods 2021; 18:1192-1195. [PMID: 34594030 DOI: 10.1038/s41592-021-01262-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
DeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learning models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained deep learning models (BioImage Model Zoo). Hence, nonexperts can easily perform common image processing tasks in life-science research with deep learning-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state of the art solutions and it is equipped with utility tools for developers to include new models. Very recently, several training frameworks have adopted the deepImageJ format to deploy their work in one of the most used softwares in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of deep learning models in life sciences applications and bioimage informatics.
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Affiliation(s)
- Estibaliz Gómez-de-Mariscal
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid and Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Carlos García-López-de-Haro
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid and Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Wei Ouyang
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Laurène Donati
- EPFL Center for Imaging, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Michael Unser
- Biomedical Imaging Group and EPFL Center for Imaging, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Arrate Muñoz-Barrutia
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid and Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
| | - Daniel Sage
- Biomedical Imaging Group and EPFL Center for Imaging, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Gómez-de-Mariscal E, Maška M, Kotrbová A, Pospíchalová V, Matula P, Muñoz-Barrutia A. Deep-Learning-Based Segmentation of Small Extracellular Vesicles in Transmission Electron Microscopy Images. Sci Rep 2019; 9:13211. [PMID: 31519998 PMCID: PMC6744556 DOI: 10.1038/s41598-019-49431-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Small extracellular vesicles (sEVs) are cell-derived vesicles of nanoscale size (~30-200 nm) that function as conveyors of information between cells, reflecting the cell of their origin and its physiological condition in their content. Valuable information on the shape and even on the composition of individual sEVs can be recorded using transmission electron microscopy (TEM). Unfortunately, sample preparation for TEM image acquisition is a complex procedure, which often leads to noisy images and renders automatic quantification of sEVs an extremely difficult task. We present a completely deep-learning-based pipeline for the segmentation of sEVs in TEM images. Our method applies a residual convolutional neural network to obtain fine masks and use the Radon transform for splitting clustered sEVs. Using three manually annotated datasets that cover a natural variability typical for sEV studies, we show that the proposed method outperforms two different state-of-the-art approaches in terms of detection and segmentation performance. Furthermore, the diameter and roundness of the segmented vesicles are estimated with an error of less than 10%, which supports the high potential of our method in biological applications.
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Affiliation(s)
- Estibaliz Gómez-de-Mariscal
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid, Leganés, 28911, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28007, Spain
| | - Martin Maška
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - Anna Kotrbová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Vendula Pospíchalová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Pavel Matula
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - Arrate Muñoz-Barrutia
- Bioengineering and Aerospace Engineering Department, Universidad Carlos III de Madrid, Leganés, 28911, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28007, Spain.
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