Deep Learning in Biomedical Image Segmentation and Classification: Advancements, Challenges and Applications, 2nd Edition

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Department of Engineering and Applied Sciences, Memorial University, St. John’s, NL A1B 3X5, Canada
Interests: machine learning; computer vision; biomedical engineering; wireless communications and networks; remote sensing
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Special Issue Information

Dear Colleagues,

This Special Issue aims to explore the latest advancements, challenges, and applications associated with deep learning techniques in the field of biomedical image segmentation and classification. Biomedical image analysis plays a crucial role in various medical domains, enabling the accurate identification, segmentation, and classification of structures, organs, and anomalies. Deep learning, with its ability to learn complex features and patterns from large-scale datasets, has revolutionized biomedical image analysis, offering significant improvements in segmentation and classification accuracy and efficiency. This Special Issue welcomes the submission of original research papers, review articles, and case studies that present novel deep learning methodologies, architectures, and algorithms, as well as their practical applications and implications in biomedical image segmentation and classification. This collection of contributions will provide a comprehensive overview of the current state-of-the-art techniques, identify challenges and limitations, and pave the way for future research directions in this rapidly evolving field.

This Special Issue is a follow up to a previous one. We appreciate the authors’ valuable contributions to the 1st edition, which can be accessed via the following link: https://www.mdpi.com/journal/jimaging/special_issues/DZ7T60VI90.

Dr. Ebrahim Karami
Guest Editor

Manuscript Submission Information

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Keywords

  • biomedical image segmentation
  • biomedical image classification
  • lesion detection with deep learning
  • cancer detection and classification with deep learning
  • computer-aided diagnosis
  • deep learning for MRI and FMRI imaging
  • deep learning for X-ray imaging
  • deep learning for ultrasound imaging
  • deep learning for infrared imaging
  • deep learning for biomedical object localization
  • biomedical image denoising and enhancement using deep learning
  • 3D and 4D biomedical image analysis
  • multimodal and multiscale biomedical data fusion
  • synthetic data generation and data augmentation
  • explainability, interpretability, and uncertainty quantification
  • ethics, bias, and federated learning in biomedical imaging

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Related Special Issue

Published Papers (2 papers)

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Research

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26 pages, 5686 KB  
Article
Cell Structure Segmentation in TEM Images of Murine Skin Melanoma Cells by Deep Learning Model
by Mikhail A. Genaev, Izabella S. Gogaeva, Iuliia S. Taskaeva, Nataliya P. Bgatova, Mikhail V. Kozhekin, Evgeniy G. Komyshev and Dmitry A. Afonnikov
J. Imaging 2026, 12(5), 215; https://doi.org/10.3390/jimaging12050215 - 18 May 2026
Abstract
Mitochondria–endoplasmic reticulum contact sites (MERCs) are known as the specialized areas that are involved in a large number of intracellular signaling pathways that regulate Ca2+ homeostasis, lipid transport, mitochondrial dynamics, cell death, and autophagy. Understanding MERC dynamics has important therapeutic implications in [...] Read more.
Mitochondria–endoplasmic reticulum contact sites (MERCs) are known as the specialized areas that are involved in a large number of intracellular signaling pathways that regulate Ca2+ homeostasis, lipid transport, mitochondrial dynamics, cell death, and autophagy. Understanding MERC dynamics has important therapeutic implications in cancer, as these contacts regulate fundamental cellular processes and MERCs represent promising targets for therapeutic interventions aimed at improving cancer treatment outcomes. Despite the accumulated data, the role of MERCs in carcinogenesis still remains unknown; thus, it seems promising to search for new tools facilitating the study of MERCs in tumor cells. The structure of MERCs can be examined in great detail using transmission electron microscopy (TEM). Currently, several hundred TEM images are required to obtain reliable data on these contacts. The speed of data processing can be significantly improved by using fast and accurate image analysis techniques based on deep learning models. In this study, five U-Net models with a ResNet34 encoder network were evaluated, including the basic U-Net-Vanilla architecture as well as models incorporating various attention blocks and blocks capturing multilevel image structure, for the segmentation of mitochondria and the endoplasmic reticulum (ER). The best performance on the test dataset was demonstrated by the U-Net-scSE network, with F1 scores of 0.872 for mitochondria and 0.744 for the ER being achieved. Two models were tested for their ability to leverage pre-training on external datasets (Lucchi++, Kasthuri++, and DeepPi-EM). Additionally, models pre-trained on the CEM500K dataset were evaluated after the parameters had been tuned on the data. It was demonstrated by the results that pre-training or the use of pre-trained networks did not lead to an improvement in the IoU and F1 metrics on the test dataset. Subsequent image analysis was conducted to assess two types of MERCs in the segmented images. Finally, the free and user-friendly UltraNet web server was developed for automated analysis of mitochondria, ER, and MERCs using TEM images. Full article
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Review

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21 pages, 1453 KB  
Review
Current Trends and Future Opportunities of AI-Based Analysis in Mesenchymal Stem Cell Imaging: A Scoping Review
by Maksim Solopov, Elizaveta Chechekhina, Viktor Turchin, Andrey Popandopulo, Dmitry Filimonov, Anzhelika Burtseva and Roman Ishchenko
J. Imaging 2025, 11(10), 371; https://doi.org/10.3390/jimaging11100371 - 18 Oct 2025
Cited by 2 | Viewed by 2452
Abstract
This scoping review explores the application of artificial intelligence (AI) methods for analyzing mesenchymal stem cells (MSCs) images. The aim of this study was to identify key areas where AI-based image processing techniques are utilized for MSCs analysis, assess their effectiveness, and highlight [...] Read more.
This scoping review explores the application of artificial intelligence (AI) methods for analyzing mesenchymal stem cells (MSCs) images. The aim of this study was to identify key areas where AI-based image processing techniques are utilized for MSCs analysis, assess their effectiveness, and highlight existing challenges. A total of 25 studies published between 2014 and 2024 were selected from six databases (PubMed, Dimensions, Scopus, Google Scholar, eLibrary, and Cochrane) for this review. The findings demonstrate that machine learning algorithms outperform traditional methods in terms of accuracy (up to 97.5%), processing speed and noninvasive capabilities. Among AI methods, convolutional neural networks (CNNs) are the most widely employed, accounting for 64% of the studies reviewed. The primary applications of AI in MSCs image analysis include cell classification (20%), segmentation and counting (20%), differentiation assessment (32%), senescence analysis (12%), and other tasks (16%). The advantages of AI methods include automation of image analysis, elimination of subjective biases, and dynamic monitoring of live cells without the need for fixation and staining. However, significant challenges persist, such as the high heterogeneity of the MSCs population, the absence of standardized protocols for AI implementation, and limited availability of annotated datasets. To advance this field, future efforts should focus on developing interpretable and multimodal AI models, creating standardized validation frameworks and open-access datasets, and establishing clear regulatory pathways for clinical translation. Addressing these challenges is crucial for accelerating the adoption of AI in MSCs biomanufacturing and enhancing the efficacy of cell therapies. Full article
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