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Din S, Mourad O, Serpedin E. LSCS-Net: A lightweight skin cancer segmentation network with densely connected multi-rate atrous convolution. Comput Biol Med 2024; 173:108303. [PMID: 38547653 DOI: 10.1016/j.compbiomed.2024.108303] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/18/2024] [Accepted: 03/12/2024] [Indexed: 04/17/2024]
Abstract
The rising occurrence and notable public health consequences of skin cancer, especially of the most challenging form known as melanoma, have created an urgent demand for more advanced approaches to disease management. The integration of modern computer vision methods into clinical procedures offers the potential for enhancing the detection of skin cancer . The UNet model has gained prominence as a valuable tool for this objective, continuously evolving to tackle the difficulties associated with the inherent diversity of dermatological images. These challenges stem from diverse medical origins and are further complicated by variations in lighting, patient characteristics, and hair density. In this work, we present an innovative end-to-end trainable network crafted for the segmentation of skin cancer . This network comprises an encoder-decoder architecture, a novel feature extraction block, and a densely connected multi-rate Atrous convolution block. We evaluated the performance of the proposed lightweight skin cancer segmentation network (LSCS-Net) on three widely used benchmark datasets for skin lesion segmentation: ISIC 2016, ISIC 2017, and ISIC 2018. The generalization capabilities of LSCS-Net are testified by the excellent performance on breast cancer and thyroid nodule segmentation datasets. The empirical findings confirm that LSCS-net attains state-of-the-art results, as demonstrated by a significantly elevated Jaccard index.
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Affiliation(s)
- Sadia Din
- Electrical and Computer Engineering Program, Texas A&M University, Doha, Qatar.
| | | | - Erchin Serpedin
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
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Xue Y, Chen X, Liu P, Lv X. HDS-Net: Achieving fine-grained skin lesion segmentation using hybrid encoding and dynamic sparse attention. PLoS One 2024; 19:e0299392. [PMID: 38512922 PMCID: PMC10956881 DOI: 10.1371/journal.pone.0299392] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/09/2024] [Indexed: 03/23/2024] Open
Abstract
Skin cancer is one of the most common malignant tumors worldwide, and early detection is crucial for improving its cure rate. In the field of medical imaging, accurate segmentation of lesion areas within skin images is essential for precise diagnosis and effective treatment. Due to the capacity of deep learning models to conduct adaptive feature learning through end-to-end training, they have been widely applied in medical image segmentation tasks. However, challenges such as boundary ambiguity between normal skin and lesion areas, significant variations in the size and shape of lesion areas, and different types of lesions in different samples pose significant obstacles to skin lesion segmentation. Therefore, this study introduces a novel network model called HDS-Net (Hybrid Dynamic Sparse Network), aiming to address the challenges of boundary ambiguity and variations in lesion areas in skin image segmentation. Specifically, the proposed hybrid encoder can effectively extract local feature information and integrate it with global features. Additionally, a dynamic sparse attention mechanism is introduced, mitigating the impact of irrelevant redundancies on segmentation performance by precisely controlling the sparsity ratio. Experimental results on multiple public datasets demonstrate a significant improvement in Dice coefficients, reaching 0.914, 0.857, and 0.898, respectively.
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Affiliation(s)
- You Xue
- College of Information Science and Engineering, Xinjiang University, Urumqi, China
| | - Xinya Chen
- College of Information Science and Engineering, Xinjiang University, Urumqi, China
| | - Pei Liu
- College of Information Science and Engineering, Xinjiang University, Urumqi, China
| | - Xiaoyi Lv
- College of Software, Xinjiang University, Urumqi, China
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3
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Fu Y, Liu J, Shi J. TSCA-Net: Transformer based spatial-channel attention segmentation network for medical images. Comput Biol Med 2024; 170:107938. [PMID: 38219644 DOI: 10.1016/j.compbiomed.2024.107938] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/21/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
Abstract
Deep learning architectures based on convolutional neural network (CNN) and Transformer have achieved great success in medical image segmentation. Models based on the encoder-decoder framework like U-Net have been successfully employed in many realistic scenarios. However, due to the low contrast between object and background, various shapes and scales of objects, and complex background in medical images, it is difficult to locate targets and obtain better segmentation performance by extracting effective information from images. In this paper, an encoder-decoder architecture based on spatial and channel attention modules built by Transformer is proposed for medical image segmentation. Concretely, spatial and channel attention modules based on Transformer are utilized to extract spatial and channel global complementary information at different layers in U-shape network, which is beneficial to learn the detail features in different scales. To fuse better spatial and channel information from Transformer features, a spatial and channel feature fusion block is designed for the decoder. The proposed network inherits the advantages of both CNN and Transformer with the local feature representation and long-range dependency for medical images. Qualitative and quantitative experiments demonstrate that the proposed method outperforms against eight state-of-the-art segmentation methods on five publicly medical image datasets including different modalities, such as 80.23% and 93.56% Dice value, 67.13% and 88.94% Intersection over Union (IoU) value on the Multi-organ Nucleus Segmentation (MoNuSeg) and Combined Healthy Abdominal Organ Segmentation with Computed Tomography scans (CHAOS-CT) datasets.
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Affiliation(s)
- Yinghua Fu
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Junfeng Liu
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Jun Shi
- School of Communication and Information Engineering, Shanghai University, Shanghai, 200444, China.
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Derekas P, Spyridonos P, Likas A, Zampeta A, Gaitanis G, Bassukas I. The Promise of Semantic Segmentation in Detecting Actinic Keratosis Using Clinical Photography in the Wild. Cancers (Basel) 2023; 15:4861. [PMID: 37835555 PMCID: PMC10571759 DOI: 10.3390/cancers15194861] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/01/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
AK is a common precancerous skin condition that requires effective detection and treatment monitoring. To improve the monitoring of the AK burden in clinical settings with enhanced automation and precision, the present study evaluates the application of semantic segmentation based on the U-Net architecture (i.e., AKU-Net). AKU-Net employs transfer learning to compensate for the relatively small dataset of annotated images and integrates a recurrent process based on convLSTM to exploit contextual information and address the challenges related to the low contrast and ambiguous boundaries of AK-affected skin regions. We used an annotated dataset of 569 clinical photographs from 115 patients with actinic keratosis to train and evaluate the model. From each photograph, patches of 512 × 512 pixels were extracted using translation lesion boxes that encompassed lesions in different positions and captured different contexts of perilesional skin. In total, 16,488 translation-augmented crops were used for training the model, and 403 lesion center crops were used for testing. To demonstrate the improvements in AK detection, AKU-Net was compared with plain U-Net and U-Net++ architectures. The experimental results highlighted the effectiveness of AKU-Net, improving upon both automation and precision over existing approaches, paving the way for more effective and reliable evaluation of actinic keratosis in clinical settings.
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Affiliation(s)
- Panagiotis Derekas
- Department of Computer Science & Engineering, School of Engineering, University of Ioannina, 45110 Ioannina, Greece; (P.D.); (A.L.)
| | - Panagiota Spyridonos
- Department of Medical Physics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Aristidis Likas
- Department of Computer Science & Engineering, School of Engineering, University of Ioannina, 45110 Ioannina, Greece; (P.D.); (A.L.)
| | - Athanasia Zampeta
- Department of Skin and Venereal Diseases, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (G.G.); (I.B.)
| | - Georgios Gaitanis
- Department of Skin and Venereal Diseases, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (G.G.); (I.B.)
| | - Ioannis Bassukas
- Department of Skin and Venereal Diseases, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (G.G.); (I.B.)
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Innani S, Dutande P, Baid U, Pokuri V, Bakas S, Talbar S, Baheti B, Guntuku SC. Generative adversarial networks based skin lesion segmentation. Sci Rep 2023; 13:13467. [PMID: 37596306 PMCID: PMC10439152 DOI: 10.1038/s41598-023-39648-8] [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] [Received: 04/23/2023] [Accepted: 07/28/2023] [Indexed: 08/20/2023] Open
Abstract
Skin cancer is a serious condition that requires accurate diagnosis and treatment. One way to assist clinicians in this task is using computer-aided diagnosis tools that automatically segment skin lesions from dermoscopic images. We propose a novel adversarial learning-based framework called Efficient-GAN (EGAN) that uses an unsupervised generative network to generate accurate lesion masks. It consists of a generator module with a top-down squeeze excitation-based compound scaled path, an asymmetric lateral connection-based bottom-up path, and a discriminator module that distinguishes between original and synthetic masks. A morphology-based smoothing loss is also implemented to encourage the network to create smooth semantic boundaries of lesions. The framework is evaluated on the International Skin Imaging Collaboration Lesion Dataset. It outperforms the current state-of-the-art skin lesion segmentation approaches with a Dice coefficient, Jaccard similarity, and accuracy of 90.1%, 83.6%, and 94.5%, respectively. We also design a lightweight segmentation framework called Mobile-GAN (MGAN) that achieves comparable performance as EGAN but with an order of magnitude lower number of training parameters, thus resulting in faster inference times for low compute resource settings.
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Affiliation(s)
- Shubham Innani
- Center of Excellence in Signal and Image Processing, Shri Guru Gobind Singhji Institute of Engineering and Technology, Nanded, Maharashtra, India.
| | - Prasad Dutande
- Center of Excellence in Signal and Image Processing, Shri Guru Gobind Singhji Institute of Engineering and Technology, Nanded, Maharashtra, India
| | - Ujjwal Baid
- Center of Excellence in Signal and Image Processing, Shri Guru Gobind Singhji Institute of Engineering and Technology, Nanded, Maharashtra, India
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, USA
| | - Venu Pokuri
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, USA
| | - Spyridon Bakas
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, USA
| | - Sanjay Talbar
- Center of Excellence in Signal and Image Processing, Shri Guru Gobind Singhji Institute of Engineering and Technology, Nanded, Maharashtra, India
| | - Bhakti Baheti
- Center of Excellence in Signal and Image Processing, Shri Guru Gobind Singhji Institute of Engineering and Technology, Nanded, Maharashtra, India
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania, Philadelphia, USA
| | - Sharath Chandra Guntuku
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, USA
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Mirikharaji Z, Abhishek K, Bissoto A, Barata C, Avila S, Valle E, Celebi ME, Hamarneh G. A survey on deep learning for skin lesion segmentation. Med Image Anal 2023; 88:102863. [PMID: 37343323 DOI: 10.1016/j.media.2023.102863] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 02/01/2023] [Accepted: 05/31/2023] [Indexed: 06/23/2023]
Abstract
Skin cancer is a major public health problem that could benefit from computer-aided diagnosis to reduce the burden of this common disease. Skin lesion segmentation from images is an important step toward achieving this goal. However, the presence of natural and artificial artifacts (e.g., hair and air bubbles), intrinsic factors (e.g., lesion shape and contrast), and variations in image acquisition conditions make skin lesion segmentation a challenging task. Recently, various researchers have explored the applicability of deep learning models to skin lesion segmentation. In this survey, we cross-examine 177 research papers that deal with deep learning-based segmentation of skin lesions. We analyze these works along several dimensions, including input data (datasets, preprocessing, and synthetic data generation), model design (architecture, modules, and losses), and evaluation aspects (data annotation requirements and segmentation performance). We discuss these dimensions both from the viewpoint of select seminal works, and from a systematic viewpoint, examining how those choices have influenced current trends, and how their limitations should be addressed. To facilitate comparisons, we summarize all examined works in a comprehensive table as well as an interactive table available online3.
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Affiliation(s)
- Zahra Mirikharaji
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Kumar Abhishek
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Alceu Bissoto
- RECOD.ai Lab, Institute of Computing, University of Campinas, Av. Albert Einstein 1251, Campinas 13083-852, Brazil
| | - Catarina Barata
- Institute for Systems and Robotics, Instituto Superior Técnico, Avenida Rovisco Pais, Lisbon 1049-001, Portugal
| | - Sandra Avila
- RECOD.ai Lab, Institute of Computing, University of Campinas, Av. Albert Einstein 1251, Campinas 13083-852, Brazil
| | - Eduardo Valle
- RECOD.ai Lab, School of Electrical and Computing Engineering, University of Campinas, Av. Albert Einstein 400, Campinas 13083-952, Brazil
| | - M Emre Celebi
- Department of Computer Science and Engineering, University of Central Arkansas, 201 Donaghey Ave., Conway, AR 72035, USA.
| | - Ghassan Hamarneh
- Medical Image Analysis Lab, School of Computing Science, Simon Fraser University, Burnaby V5A 1S6, Canada.
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Hasan MK, Ahamad MA, Yap CH, Yang G. A survey, review, and future trends of skin lesion segmentation and classification. Comput Biol Med 2023; 155:106624. [PMID: 36774890 DOI: 10.1016/j.compbiomed.2023.106624] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/04/2023] [Accepted: 01/28/2023] [Indexed: 02/03/2023]
Abstract
The Computer-aided Diagnosis or Detection (CAD) approach for skin lesion analysis is an emerging field of research that has the potential to alleviate the burden and cost of skin cancer screening. Researchers have recently indicated increasing interest in developing such CAD systems, with the intention of providing a user-friendly tool to dermatologists to reduce the challenges encountered or associated with manual inspection. This article aims to provide a comprehensive literature survey and review of a total of 594 publications (356 for skin lesion segmentation and 238 for skin lesion classification) published between 2011 and 2022. These articles are analyzed and summarized in a number of different ways to contribute vital information regarding the methods for the development of CAD systems. These ways include: relevant and essential definitions and theories, input data (dataset utilization, preprocessing, augmentations, and fixing imbalance problems), method configuration (techniques, architectures, module frameworks, and losses), training tactics (hyperparameter settings), and evaluation criteria. We intend to investigate a variety of performance-enhancing approaches, including ensemble and post-processing. We also discuss these dimensions to reveal their current trends based on utilization frequencies. In addition, we highlight the primary difficulties associated with evaluating skin lesion segmentation and classification systems using minimal datasets, as well as the potential solutions to these difficulties. Findings, recommendations, and trends are disclosed to inform future research on developing an automated and robust CAD system for skin lesion analysis.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Bioengineering, Imperial College London, UK; Department of Electrical and Electronic Engineering (EEE), Khulna University of Engineering & Technology (KUET), Khulna 9203, Bangladesh.
| | - Md Asif Ahamad
- Department of Electrical and Electronic Engineering (EEE), Khulna University of Engineering & Technology (KUET), Khulna 9203, Bangladesh.
| | - Choon Hwai Yap
- Department of Bioengineering, Imperial College London, UK.
| | - Guang Yang
- National Heart and Lung Institute, Imperial College London, UK; Cardiovascular Research Centre, Royal Brompton Hospital, UK.
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