Deep Learning‐Based Single‐Cell Optical Image Studies

• Published in: Cytometry. Part A Vol. 97; no. 3; pp. 226 - 240
• Main Authors: Sun, Jing, Tárnok, Attila, Su, Xuantao
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.03.2020; Wiley Subscription Services, Inc
• Subjects: biomedical image analysis, single‐cell analysis, image cytometry, optical microscopy, deep learning, convolutional neural network; Data analysis; Data processing; Deep learning; Feasibility studies; Flow cytometry; Image analysis; Image processing; Image reconstruction; Image segmentation; Imaging techniques; Learning algorithms; Machine learning; Task complexity; Test methods; Transfer learning; biomedical image analysis, single-cell analysis, image cytometry, optical microscopy, deep learning, convolutional neural network
• ISSN: 1552-4922; 1552-4930; 1552-4930
• DOI: 10.1002/cyto.a.23973

Optical imaging technology that has the advantages of high sensitivity and cost‐effectiveness greatly promotes the progress of nondestructive single‐cell studies. Complex cellular image analysis tasks such as three‐dimensional reconstruction call for machine‐learning technology in cell optical image research. With the rapid developments of high‐throughput imaging flow cytometry, big data cell optical images are always obtained that may require machine learning for data analysis. In recent years, deep learning has been prevalent in the field of machine learning for large‐scale image processing and analysis, which brings a new dawn for single‐cell optical image studies with an explosive growth of data availability. Popular deep learning techniques offer new ideas for multimodal and multitask single‐cell optical image research. This article provides an overview of the basic knowledge of deep learning and its applications in single‐cell optical image studies. We explore the feasibility of applying deep learning techniques to single‐cell optical image analysis, where popular techniques such as transfer learning, multimodal learning, multitask learning, and end‐to‐end learning have been reviewed. Image preprocessing and deep learning model training methods are then summarized. Applications based on deep learning techniques in the field of single‐cell optical image studies are reviewed, which include image segmentation, super‐resolution image reconstruction, cell tracking, cell counting, cross‐modal image reconstruction, and design and control of cell imaging systems. In addition, deep learning in popular single‐cell optical imaging techniques such as label‐free cell optical imaging, high‐content screening, and high‐throughput optical imaging cytometry are also mentioned. Finally, the perspectives of deep learning technology for single‐cell optical image analysis are discussed. © 2020 International Society for Advancement of Cytometry