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Vanhoucke T, Perima A, Zolfanelli L, Bruhns P, Broketa M. Deep learning enabled label-free microfluidic droplet classification for single cell functional assays. Front Bioeng Biotechnol 2024; 12:1468738. [PMID: 39359262 PMCID: PMC11445169 DOI: 10.3389/fbioe.2024.1468738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/30/2024] [Indexed: 10/04/2024] Open
Abstract
Droplet-based microfluidics techniques coupled to microscopy allow for the characterization of cells at the single-cell scale. However, such techniques generate substantial amounts of data and microscopy images that must be analyzed. Droplets on these images usually need to be classified depending on the number of cells they contain. This verification, when visually carried out by the experimenter image-per-image, is time-consuming and impractical for analysis of many assays or when an assay yields many putative droplets of interest. Machine learning models have already been developed to classify cell-containing droplets within microscopy images, but not in the context of assays in which non-cellular structures are present inside the droplet in addition to cells. Here we develop a deep learning model using the neural network ResNet-50 that can be applied to functional droplet-based microfluidic assays to classify droplets according to the number of cells they contain with >90% accuracy in a very short time. This model performs high accuracy classification of droplets containing both cells with non-cellular structures and cells alone and can accommodate several different cell types, for generalization to a broader array of droplet-based microfluidics applications.
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Affiliation(s)
- Thibault Vanhoucke
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Angga Perima
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
| | - Lorenzo Zolfanelli
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
- Laboratoire de Colloides et Matériaux Divisés, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, Université Paris Sciences et Lettres, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 8231, Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
- Paris Est Créteil University (UPEC), Assistance Publique-Hôpitaux de Paris (AP-HP), Henri Mondor Hospital, Fédération Hospitalo-Universitaire TRUE InnovaTive theRapy for immUne disordErs, Créteil, France
| | - Matteo Broketa
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Evexta Bio, Paris, France
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Kim J, Lee SJ. Digital in-line holographic microscopy for label-free identification and tracking of biological cells. Mil Med Res 2024; 11:38. [PMID: 38867274 PMCID: PMC11170804 DOI: 10.1186/s40779-024-00541-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Digital in-line holographic microscopy (DIHM) is a non-invasive, real-time, label-free technique that captures three-dimensional (3D) positional, orientational, and morphological information from digital holographic images of living biological cells. Unlike conventional microscopies, the DIHM technique enables precise measurements of dynamic behaviors exhibited by living cells within a 3D volume. This review outlines the fundamental principles and comprehensive digital image processing procedures employed in DIHM-based cell tracking methods. In addition, recent applications of DIHM technique for label-free identification and digital tracking of various motile biological cells, including human blood cells, spermatozoa, diseased cells, and unicellular microorganisms, are thoroughly examined. Leveraging artificial intelligence has significantly enhanced both the speed and accuracy of digital image processing for cell tracking and identification. The quantitative data on cell morphology and dynamics captured by DIHM can effectively elucidate the underlying mechanisms governing various microbial behaviors and contribute to the accumulation of diagnostic databases and the development of clinical treatments.
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Affiliation(s)
- Jihwan Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Sang Joon Lee
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea.
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Khan RU, Almakdi S, Alshehri M, Haq AU, Ullah A, Kumar R. An intelligent neural network model to detect red blood cells for various blood structure classification in microscopic medical images. Heliyon 2024; 10:e26149. [PMID: 38384569 PMCID: PMC10879026 DOI: 10.1016/j.heliyon.2024.e26149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
Biomedical image analysis plays a crucial role in enabling high-performing imaging and various clinical applications. For the proper diagnosis of blood diseases related to red blood cells, red blood cells must be accurately identified and categorized. Manual analysis is time-consuming and prone to mistakes. Analyzing multi-label samples, which contain clusters of cells, is challenging due to difficulties in separating individual cells, such as touching or overlapping cells. High-performance biomedical imaging and several medical applications are made possible by advanced biosensors. We develop an intelligent neural network model that can automatically identify and categorize red blood cells from microscopic medical images using region-based convolutional neural networks (RCNN) and cutting-edge biosensors. Our model successfully navigates obstacles like touching or overlapping cells and accurately recognizes various blood structures. Additionally, we utilized data augmentation as a pre-processing method on microscopic images to enhance the model's computational efficiency and expand the sample size. To refine the data and eliminate noise from the dataset, we utilized the Radial Gradient Index filtering algorithm for imaging data equalization. We exhibit improved detection accuracy and a reduced model loss rate when using medical imagery datasets to apply our proposed model in comparison to existing ResNet and GoogleNet models. Our model precisely detected red blood cells in a collection of medical images with 99% training accuracy and 91.21% testing accuracy. Our proposed model outperformed earlier models like ResNet-50 and GoogleNet by 10-15%. Our results demonstrated that Artificial intelligence (AI)-assisted automated red blood cell detection has the potential to revolutionize and speed up blood cell analysis, minimizing human error and enabling early illness diagnosis.
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Affiliation(s)
- Riaz Ullah Khan
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China
| | - Sultan Almakdi
- Department of Computer Science, College of Computer Science and Information systems, Najran University, Najran 55461, Saudi Arabia
| | - Mohammed Alshehri
- Department of Computer Science, College of Computer Science and Information systems, Najran University, Najran 55461, Saudi Arabia
| | - Amin Ul Haq
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Aman Ullah
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China
| | - Rajesh Kumar
- Yangtze Delta Region Institute (Huzhou), University of Electronic Science and Technology of China, Huzhou 313001, China
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