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Mochalova EN, Kotov IA, Lifanov DA, Chakraborti S, Nikitin MP. Imaging flow cytometry data analysis using convolutional neural network for quantitative investigation of phagocytosis. Biotechnol Bioeng 2021; 119:626-635. [PMID: 34750809 DOI: 10.1002/bit.27986] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 01/03/2023]
Abstract
Macrophages play an important role in the adaptive immune system. Their ability to neutralize cellular targets through Fc receptor-mediated phagocytosis has relied upon immunotherapy that has become of particular interest for the treatment of cancer and autoimmune diseases. A detailed investigation of phagocytosis is the key to the improvement of the therapeutic efficiency of existing medications and the creation of new ones. A promising method for studying the process is imaging flow cytometry (IFC) that acquires thousands of cell images per second in up to 12 optical channels and allows multiparametric fluorescent and morphological analysis of samples in the flow. However, conventional IFC data analysis approaches are based on a highly subjective manual choice of masks and other processing parameters that can lead to the loss of valuable information embedded in the original image. Here, we show the application of a Faster region-based convolutional neural network (CNN) for accurate quantitative analysis of phagocytosis using imaging flow cytometry data. Phagocytosis of erythrocytes by peritoneal macrophages was chosen as a model system. CNN performed automatic high-throughput processing of datasets and demonstrated impressive results in the identification and classification of macrophages and erythrocytes, despite the variety of shapes, sizes, intensities, and textures of cells in images. The developed procedure allows determining the number of phagocytosed cells, disregarding cases with a low probability of correct classification. We believe that CNN-based approaches will enable powerful in-depth investigation of a wide range of biological processes and will reveal the intricate nature of heterogeneous objects in images, leading to completely new capabilities in diagnostics and therapy.
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Affiliation(s)
- Elizaveta N Mochalova
- Nanobiotechnology Laboratory, Moscow Institute of Physics and Technology, Moscow, Russia.,Biophotonics Laboratory, Prokhorov General Physics Institute of the Russian Academy of Sciences, Moscow, Russia.,Nanobiomedicine Division, Sirius University of Science and Technology, Sochi, Russia
| | - Ivan A Kotov
- Nanobiotechnology Laboratory, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Dmitry A Lifanov
- Nanobiotechnology Laboratory, Moscow Institute of Physics and Technology, Moscow, Russia
| | | | - Maxim P Nikitin
- Nanobiotechnology Laboratory, Moscow Institute of Physics and Technology, Moscow, Russia.,Nanobiomedicine Division, Sirius University of Science and Technology, Sochi, Russia
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Lakstygal AM, de Abreu MS, Lifanov DA, Wappler-Guzzetta EA, Serikuly N, Alpsyshov ET, Wang D, Wang M, Tang Z, Yan D, Demin KA, Volgin AD, Amstislavskaya TG, Wang J, Song C, Alekseeva P, Kalueff AV. Zebrafish models of diabetes-related CNS pathogenesis. Prog Neuropsychopharmacol Biol Psychiatry 2019; 92:48-58. [PMID: 30476525 DOI: 10.1016/j.pnpbp.2018.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/18/2018] [Accepted: 11/22/2018] [Indexed: 12/12/2022]
Abstract
Diabetes mellitus (DM) is a common metabolic disorder that affects multiple organ systems. DM also affects brain processes, contributing to various CNS disorders, including depression, anxiety and Alzheimer's disease. Despite active research in humans, rodent models and in-vitro systems, the pathogenetic link between DM and brain disorders remains poorly understood. Novel translational models and new model organisms are therefore essential to more fully study the impact of DM on CNS. The zebrafish (Danio rerio) is a powerful novel model species to study metabolic and CNS disorders. Here, we discuss how DM alters brain functions and behavior in zebrafish, and summarize their translational relevance to studying DM-related CNS pathogenesis in humans. We recognize the growing utility of zebrafish models in translational DM research, as they continue to improve our understanding of different brain pathologies associated with DM, and may foster the discovery of drugs that prevent or treat these diseases.
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Affiliation(s)
- Anton M Lakstygal
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia
| | - Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo (UPF), Passo Fundo, RS, Brazil; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Dmitry A Lifanov
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Laboratory of Preclinical Bioscreening, Granov Russian Research Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia; School of Pharmacy, Southwest University, Chongqing, China
| | | | - Nazar Serikuly
- School of Pharmacy, Southwest University, Chongqing, China
| | | | - DongMei Wang
- School of Pharmacy, Southwest University, Chongqing, China
| | - MengYao Wang
- School of Pharmacy, Southwest University, Chongqing, China
| | - ZhiChong Tang
- School of Pharmacy, Southwest University, Chongqing, China
| | - DongNi Yan
- School of Pharmacy, Southwest University, Chongqing, China
| | - Konstantin A Demin
- Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Andrey D Volgin
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia
| | | | - JiaJia Wang
- Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, China; Marine Medicine Development Center, Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
| | - Cai Song
- Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, China; Marine Medicine Development Center, Shenzhen Institute, Guangdong Ocean University, Shenzhen, China
| | - Polina Alekseeva
- Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China; Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; Ural Federal University, Ekaterinburg, Russia; Russian Scientific Center of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, Pesochny, Russia; ZENEREI Research Center, Slidell, LA, USA.
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