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Chang S, Marsh JF, Koons EK, Gong H, McCollough CH, Leng S. Improved noise reduction in photon-counting detector CT using prior knowledge-aware iterative denoising neural network. J Med Imaging (Bellingham) 2024; 11:S12804. [PMID: 38799270 PMCID: PMC11124219 DOI: 10.1117/1.jmi.11.s1.s12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/10/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Purpose We aim to reduce image noise in high-resolution (HR) virtual monoenergetic images (VMIs) from photon-counting detector (PCD) CT scans by developing a prior knowledge-aware iterative denoising neural network (PKAID-Net) that efficiently exploits the unique noise characteristics of VMIs at different energy (keV) levels. Approach PKAID-Net offers two major features: first, it utilizes a lower-noise VMI (e.g., 70 keV) as a prior input; second, it iteratively constructs a refined training dataset to improve the neural network's denoising performance. In each iteration, the denoised image from the previous module serves as an updated target image, which is included in the dataset for the subsequent training iteration. Our study includes 10 patient coronary CT angiography exams acquired on a clinical dual-source PCD-CT (NAEOTOM Alpha, Siemens Healthineers). The HR VMIs were reconstructed at 50, 70, and 100 keV, using a sharp vascular kernel (Bv68) and thin (0.6 mm) slice thickness (0.3 mm increment). PKAID-Net's performance was evaluated in terms of image noise, spatial detail preservation, and quantitative accuracy. Results PKAID-Net achieved a noise reduction of 96% compared to filtered back projection and 65% relative to iterative reconstruction, all while preserving spatial and spectral fidelity and maintaining a natural noise texture. The iterative refinement of PCD-CT data during the training process substantially enhanced the robustness of deep learning-based denoising compared to the original method, which resulted in some spatial detail loss. Conclusions The PKAID-Net provides substantial noise reduction while maintaining spatial and spectral fidelity of the HR VMIs from PCD-CT.
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Affiliation(s)
- Shaojie Chang
- Mayo Clinic, Department of Radiology, Rochester, Minnesota, United States
| | - Jeffrey F. Marsh
- Mayo Clinic, Department of Radiology, Rochester, Minnesota, United States
| | - Emily K. Koons
- Mayo Clinic, Department of Radiology, Rochester, Minnesota, United States
| | - Hao Gong
- Mayo Clinic, Department of Radiology, Rochester, Minnesota, United States
| | | | - Shuai Leng
- Mayo Clinic, Department of Radiology, Rochester, Minnesota, United States
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Choi K. Self-supervised learning for CT image denoising and reconstruction: a review. Biomed Eng Lett 2024; 14:1207-1220. [PMID: 39465103 PMCID: PMC11502646 DOI: 10.1007/s13534-024-00424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 10/29/2024] Open
Abstract
This article reviews the self-supervised learning methods for CT image denoising and reconstruction. Currently, deep learning has become a dominant tool in medical imaging as well as computer vision. In particular, self-supervised learning approaches have attracted great attention as a technique for learning CT images without clean/noisy references. After briefly reviewing the fundamentals of CT image denoising and reconstruction, we examine the progress of deep learning in CT image denoising and reconstruction. Finally, we focus on the theoretical and methodological evolution of self-supervised learning for image denoising and reconstruction.
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Affiliation(s)
- Kihwan Choi
- Department of Applied Artificial Intelligence, Seoul National University of Science and Technology, 232 Gongneung-ro, Nowon-gu, Seoul, 01811 Republic of Korea
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Zhao F, Liu M, Xiang M, Li D, Jiang X, Jin X, Lin C, Wang R. Unsupervised and Self-supervised Learning in Low-Dose Computed Tomography Denoising: Insights from Training Strategies. JOURNAL OF IMAGING INFORMATICS IN MEDICINE 2024:10.1007/s10278-024-01213-8. [PMID: 39231886 DOI: 10.1007/s10278-024-01213-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 09/06/2024]
Abstract
In recent years, X-ray low-dose computed tomography (LDCT) has garnered widespread attention due to its significant reduction in the risk of patient radiation exposure. However, LDCT images often contain a substantial amount of noises, adversely affecting diagnostic quality. To mitigate this, a plethora of LDCT denoising methods have been proposed. Among them, deep learning (DL) approaches have emerged as the most effective, due to their robust feature extraction capabilities. Yet, the prevalent use of supervised training paradigms is often impractical due to the challenges in acquiring low-dose and normal-dose CT pairs in clinical settings. Consequently, unsupervised and self-supervised deep learning methods have been introduced for LDCT denoising, showing considerable potential for clinical applications. These methods' efficacy hinges on training strategies. Notably, there appears to be no comprehensive reviews of these strategies. Our review aims to address this gap, offering insights and guidance for researchers and practitioners. Based on training strategies, we categorize the LDCT methods into six groups: (i) cycle consistency-based, (ii) score matching-based, (iii) statistical characteristics of noise-based, (iv) similarity-based, (v) LDCT synthesis model-based, and (vi) hybrid methods. For each category, we delve into the theoretical underpinnings, training strategies, strengths, and limitations. In addition, we also summarize the open source codes of the reviewed methods. Finally, the review concludes with a discussion on open issues and future research directions.
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Affiliation(s)
- Feixiang Zhao
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Ouhai District, Wenzhou, 325000, Zhejiang, China
- College of Nuclear Technology and Automation Engineering, Chengdu University of Technology, 1 East Third Road, Chengdu, 610059, Sichuan, China
| | - Mingzhe Liu
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Ouhai District, Wenzhou, 325000, Zhejiang, China
- College of Computer Science and Cyber Security, Chengdu University of Technology, 1 East Third Road, Chengdu, 610059, Sichuan, China
| | - Mingrong Xiang
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Ouhai District, Wenzhou, 325000, Zhejiang, China.
- School of Information Technology, Deakin University, Melbourne Burwood Campus, 221 Burwood Hwy, Melbourne, 3125, Victoria, Australia.
| | - Dongfen Li
- College of Computer Science and Cyber Security, Chengdu University of Technology, 1 East Third Road, Chengdu, 610059, Sichuan, China
| | - Xin Jiang
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Ouhai District, Wenzhou, 325000, Zhejiang, China
| | - Xiance Jin
- Department of Radiotherapy Center, The first Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou, 325000, Zhejiang, China
| | - Cai Lin
- Department of Burn, Wound Repair and Regenerative Medicine Center, The first Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou, 325000, Zhejiang, China
| | - Ruili Wang
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Ouhai District, Wenzhou, 325000, Zhejiang, China
- School of Mathematical and Computational Science, Massey University, SH17, Albany, 0632, Auckland, New Zealand
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Ko Y, Song S, Baek J, Shim H. Adapting low-dose CT denoisers for texture preservation using zero-shot local noise-level matching. Med Phys 2024; 51:4181-4200. [PMID: 38478305 DOI: 10.1002/mp.17015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 01/27/2024] [Accepted: 01/28/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND On enhancing the image quality of low-dose computed tomography (LDCT), various denoising methods have achieved meaningful improvements. However, they commonly produce over-smoothed results; the denoised images tend to be more blurred than the normal-dose targets (NDCTs). Furthermore, many recent denoising methods employ deep learning(DL)-based models, which require a vast amount of CT images (or image pairs). PURPOSE Our goal is to address the problem of over-smoothed results and design an algorithm that works regardless of the need for a large amount of training dataset to achieve plausible denoising results. Over-smoothed images negatively affect the diagnosis and treatment since radiologists had developed clinical experiences with NDCT. Besides, a large-scale training dataset is often not available in clinical situations. To overcome these limitations, we propose locally-adaptive noise-level matching (LANCH), emphasizing the output should retain the same noise-level and characteristics to that of the NDCT without additional training. METHODS We represent the NDCT image as the pixel-wisely weighted sum of an over-smoothed output from off-the-shelf denoiser (OSD) and the difference between the LDCT image and the OSD output. Herein, LANCH determines a 2D ratio map (i.e., pixel-wise weight matrix) by locally matching the noise-level of output and NDCT, where the LDCT-to-NDCT device flux (mAs) ratio reveals the NDCT noise-level. Thereby, LANCH can preserve important details in LDCT, and enhance the sharpness of the noise-free regions. Note that LANCH can enhance any LDCT denoisers without additional training data (i.e., zero-shot). RESULTS The proposed method is applicable to any OSD denoisers, reporting significant texture plausibility development over the baseline denoisers in quantitative and qualitative manners. It is surprising that the denoising accuracy achieved by our method with zero-shot denoiser was comparable or superior to that of the best training-based denoisers; our result showed 1% and 33% gains in terms of SSIM and DISTS, respectively. Reader study with experienced radiologists shows significant image quality improvements, a gain of + 1.18 on a five-point mean opinion score scale. CONCLUSIONS In this paper, we propose a technique to enhance any low-dose CT denoiser by leveraging the fundamental physical relationship between the x-ray flux and noise variance. Our method is capable of operating in a zero-shot condition, which means that only a single low-dose CT image is required for the enhancement process. We demonstrate that our approach is comparable or even superior to supervised DL-based denoisers that are trained using numerous CT images. Extensive experiments illustrate that our method consistently improves the performance of all tested LDCT denoisers.
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Affiliation(s)
- Youngjun Ko
- School of Integrated Technology, Yonsei University, Incheon, South Korea
| | - Seongjong Song
- School of Integrated Technology, Yonsei University, Incheon, South Korea
| | - Jongduk Baek
- School of Integrated Technology, Yonsei University, Incheon, South Korea
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Kim W, Lee J, Choi JH. An unsupervised two-step training framework for low-dose computed tomography denoising. Med Phys 2024; 51:1127-1144. [PMID: 37432026 DOI: 10.1002/mp.16628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/25/2023] [Accepted: 06/25/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Although low-dose computed tomography (CT) imaging has been more widely adopted in clinical practice to reduce radiation exposure to patients, the reconstructed CT images tend to have more noise, which impedes accurate diagnosis. Recently, deep neural networks using convolutional neural networks to reduce noise in the reconstructed low-dose CT images have shown considerable improvement. However, they need a large number of paired normal- and low-dose CT images to fully train the network via supervised learning methods. PURPOSE To propose an unsupervised two-step training framework for image denoising that uses low-dose CT images of one dataset and unpaired high-dose CT images from another dataset. METHODS Our proposed framework trains the denoising network in two steps. In the first training step, we train the network using 3D volumes of CT images and predict the center CT slice from them. This pre-trained network is used in the second training step to train the denoising network and is combined with the memory-efficient denoising generative adversarial network (DenoisingGAN), which further enhances both objective and perceptual quality. RESULTS The experimental results on phantom and clinical datasets show superior performance over the existing traditional machine learning and self-supervised deep learning methods, and the results are comparable to the fully supervised learning methods. CONCLUSIONS We proposed a new unsupervised learning framework for low-dose CT denoising, convincingly improving noisy CT images from both objective and perceptual quality perspectives. Because our denoising framework does not require physics-based noise models or system-dependent assumptions, our proposed method can be easily reproduced; consequently, it can also be generally applicable to various CT scanners or dose levels.
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Affiliation(s)
- Wonjin Kim
- Division of Mechanical and Biomedical Engineering, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jaayeon Lee
- Division of Mechanical and Biomedical Engineering, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jang-Hwan Choi
- Division of Mechanical and Biomedical Engineering, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
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Sadia RT, Chen J, Zhang J. CT image denoising methods for image quality improvement and radiation dose reduction. J Appl Clin Med Phys 2024; 25:e14270. [PMID: 38240466 PMCID: PMC10860577 DOI: 10.1002/acm2.14270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/15/2023] [Accepted: 12/28/2023] [Indexed: 02/13/2024] Open
Abstract
With the ever-increasing use of computed tomography (CT), concerns about its radiation dose have become a significant public issue. To address the need for radiation dose reduction, CT denoising methods have been widely investigated and applied in low-dose CT images. Numerous noise reduction algorithms have emerged, such as iterative reconstruction and most recently, deep learning (DL)-based approaches. Given the rapid advancements in Artificial Intelligence techniques, we recognize the need for a comprehensive review that emphasizes the most recently developed methods. Hence, we have performed a thorough analysis of existing literature to provide such a review. Beyond directly comparing the performance, we focus on pivotal aspects, including model training, validation, testing, generalizability, vulnerability, and evaluation methods. This review is expected to raise awareness of the various facets involved in CT image denoising and the specific challenges in developing DL-based models.
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Affiliation(s)
- Rabeya Tus Sadia
- Department of Computer ScienceUniversity of KentuckyLexingtonKentuckyUSA
| | - Jin Chen
- Department of Medicine‐NephrologyUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Jie Zhang
- Department of RadiologyUniversity of KentuckyLexingtonKentuckyUSA
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Choi K, Kim SH, Kim S. Self-supervised denoising of projection data for low-dose cone-beam CT. Med Phys 2023; 50:6319-6333. [PMID: 37079443 DOI: 10.1002/mp.16421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Convolutional neural networks (CNNs) have shown promising results in image denoising tasks. While most existing CNN-based methods depend on supervised learning by directly mapping noisy inputs to clean targets, high-quality references are often unavailable for interventional radiology such as cone-beam computed tomography (CBCT). PURPOSE In this paper, we propose a novel self-supervised learning method that reduces noise in projections acquired by ordinary CBCT scans. METHODS With a network that partially blinds input, we are able to train the denoising model by mapping the partially blinded projections to the original projections. Additionally, we incorporate noise-to-noise learning into the self-supervised learning by mapping the adjacent projections to the original projections. With standard image reconstruction methods such as FDK-type algorithms, we can reconstruct high-quality CBCT images from the projections denoised by our projection-domain denoising method. RESULTS In the head phantom study, we measure peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) values of the proposed method along with the other denoising methods and uncorrected low-dose CBCT data for a quantitative comparison both in projection and image domains. The PSNR and SSIM values of our self-supervised denoising approach are 27.08 and 0.839, whereas those of uncorrected CBCT images are 15.68 and 0.103, respectively. In the retrospective study, we assess the quality of interventional patient CBCT images to evaluate the projection-domain and image-domain denoising methods. Both qualitative and quantitative results indicate that our approach can effectively produce high-quality CBCT images with low-dose projections in the absence of duplicate clean or noisy references. CONCLUSIONS Our self-supervised learning strategy is capable of restoring anatomical information while efficiently removing noise in CBCT projection data.
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Affiliation(s)
- Kihwan Choi
- Bionics Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Seung Hyoung Kim
- Department of Radiology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sungwon Kim
- Department of Radiology, Yonsei University College of Medicine, Seoul, Republic of Korea
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Chang S, Huber NR, Marsh JF, Koons EK, Gong H, Yu L, McCollough CH, Leng S. Pie-Net: Prior-information-enabled deep learning noise reduction for coronary CT angiography acquired with a photon counting detector CT. Med Phys 2023; 50:6283-6295. [PMID: 37042049 PMCID: PMC10564970 DOI: 10.1002/mp.16411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/10/2023] [Accepted: 03/29/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Photon-counting-detector CT (PCD-CT) enables the production of virtual monoenergetic images (VMIs) at a high spatial resolution (HR) via simultaneous acquisition of multi-energy data. However, noise levels in these HR VMIs are markedly increased. PURPOSE To develop a deep learning technique that utilizes a lower noise VMI as prior information to reduce image noise in HR, PCD-CT coronary CT angiography (CTA). METHODS Coronary CTA exams of 10 patients were acquired using PCD-CT (NAEOTOM Alpha, Siemens Healthineers). A prior-information-enabled neural network (Pie-Net) was developed, treating one lower-noise VMI (e.g., 70 keV) as a prior input and one noisy VMI (e.g., 50 keV or 100 keV) as another. For data preprocessing, noisy VMIs were reconstructed by filtered back-projection (FBP) and iterative reconstruction (IR), which were then subtracted to generate "noise-only" images. Spatial decoupling was applied to the noise-only images to mitigate overfitting and improve randomization. Thicker slice averaging was used for the IR and prior images. The final training inputs for the convolutional neural network (CNN) inside the Pie-Net consisted of thicker-slice signal images with the reinsertion of spatially decoupled noise-only images and the thicker-slice prior images. The CNN training labels consisted of the corresponding thicker-slice label images without noise insertion. Pie-Net's performance was evaluated in terms of image noise, spatial detail preservation, and quantitative accuracy, and compared to a U-net-based method that did not include prior information. RESULTS Pie-Net provided strong noise reduction, by 95 ± 1% relative to FBP and by 60 ± 8% relative to IR. For HR VMIs at different keV (e.g., 50 keV or 100 keV), Pie-Net maintained spatial and spectral fidelity. The inclusion of prior information from the PCD-CT data in the spectral domain was able to improve a robust deep learning-based denoising performance compared to the U-net-based method, which caused some loss of spatial detail and introduced some artifacts. CONCLUSION The proposed Pie-Net achieved substantial noise reduction while preserving HR VMI's spatial and spectral properties.
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Affiliation(s)
- Shaojie Chang
- Department of Radiology, Mayo Clinic, Rochester, MN, US
| | | | | | | | - Hao Gong
- Department of Radiology, Mayo Clinic, Rochester, MN, US
| | - Lifeng Yu
- Department of Radiology, Mayo Clinic, Rochester, MN, US
| | | | - Shuai Leng
- Department of Radiology, Mayo Clinic, Rochester, MN, US
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Lepcha DC, Dogra A, Goyal B, Goyal V, Kukreja V, Bavirisetti DP. A constructive non-local means algorithm for low-dose computed tomography denoising with morphological residual processing. PLoS One 2023; 18:e0291911. [PMID: 37756296 PMCID: PMC10529561 DOI: 10.1371/journal.pone.0291911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Low-dose computed tomography (LDCT) has attracted significant attention in the domain of medical imaging due to the inherent risks of normal-dose computed tomography (NDCT) based X-ray radiations to patients. However, reducing radiation dose in CT imaging produces noise and artifacts that degrade image quality and subsequently hinders medical disease diagnostic performance. In order to address these problems, this research article presents a competent low-dose computed tomography image denoising algorithm based on a constructive non-local means algorithm with morphological residual processing to achieve the task of removing noise from the LDCT images. We propose an innovative constructive non-local image filtering algorithm by means of applications in low-dose computed tomography technology. The nonlocal mean filter that was recently proposed was modified to construct our denoising algorithm. It constructs the discrete property of neighboring filtering to enable rapid vectorized and parallel implantation in contemporary shared memory computer platforms while simultaneously decreases computing complexity. Subsequently, the proposed method performs faster computation compared to a non-vectorized and serial implementation in terms of speed and scales linearly with image dimension. In addition, the morphological residual processing is employed for the purpose of edge-preserving image processing. It combines linear lowpass filtering with a nonlinear technique that enables the extraction of meaningful regions where edges could be preserved while removing residual artifacts from the images. Experimental results demonstrate that the proposed algorithm preserves more textural and structural features while reducing noise, enhances edges and significantly improves image quality more effectively. The proposed research article obtains better results both qualitatively and quantitively when compared to other comparative algorithms on publicly accessible datasets.
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Affiliation(s)
| | - Ayush Dogra
- Chitkara University Institute of Engineering and Technology, Chitkara University, Punjab, India
| | - Bhawna Goyal
- Department of ECE and UCRD, Chandigarh University, Mohali, Punjab, India
| | | | - Vinay Kukreja
- Chitkara University Institute of Engineering and Technology, Chitkara University, Punjab, India
| | - Durga Prasad Bavirisetti
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
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Wang Z, Liu M, Cheng X, Zhu J, Wang X, Gong H, Liu M, Xu L. Self-adaption and texture generation: A hybrid loss function for low-dose CT denoising. J Appl Clin Med Phys 2023; 24:e14113. [PMID: 37571834 PMCID: PMC10476999 DOI: 10.1002/acm2.14113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 05/25/2023] [Accepted: 07/11/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Deep learning has been successfully applied to low-dose CT (LDCT) denoising. But the training of the model is very dependent on an appropriate loss function. Existing denoising models often use per-pixel loss, including mean abs error (MAE) and mean square error (MSE). This ignores the difference in denoising difficulty between different regions of the CT images and leads to the loss of large texture information in the generated image. PURPOSE In this paper, we propose a new hybrid loss function that adapts to the noise in different regions of CT images to balance the denoising difficulty and preserve texture details, thus acquiring CT images with high-quality diagnostic value using LDCT images, providing strong support for condition diagnosis. METHODS We propose a hybrid loss function consisting of weighted patch loss (WPLoss) and high-frequency information loss (HFLoss). To enhance the model's denoising ability of the local areas which are difficult to denoise, we improve the MAE to obtain WPLoss. After the generated image and the target image are divided into several patches, the loss weight of each patch is adaptively and dynamically adjusted according to its loss ratio. In addition, considering that texture details are contained in the high-frequency information of the image, we use HFLoss to calculate the difference between CT images in the high-frequency information part. RESULTS Our hybrid loss function improves the denoising performance of several models in the experiment, and obtains a higher peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM). Moreover, through visual inspection of the generated results of the comparison experiment, the proposed hybrid function can effectively suppress noise and retain image details. CONCLUSIONS We propose a hybrid loss function for LDCT image denoising, which has good interpretation properties and can improve the denoising performance of existing models. And the validation results of multiple models using different datasets show that it has good generalization ability. By using this loss function, high-quality CT images with low radiation are achieved, which can avoid the hazards caused by radiation and ensure the disease diagnosis for patients.
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Affiliation(s)
- Zhenchuan Wang
- Yangtze Delta Region Institute(Quzhou), University of Electronic Science and Technology of ChinaQuzhouChina
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's HospitalQuzhouChina
| | - Minghui Liu
- Yangtze Delta Region Institute(Quzhou), University of Electronic Science and Technology of ChinaQuzhouChina
- University of Electronic Science and Technology of ChinaChengduChina
| | - Xuan Cheng
- Yangtze Delta Region Institute(Quzhou), University of Electronic Science and Technology of ChinaQuzhouChina
- University of Electronic Science and Technology of ChinaChengduChina
| | - Jinqi Zhu
- Tianjin Normal UniversityTianjinChina
| | - Xiaomin Wang
- Yangtze Delta Region Institute(Quzhou), University of Electronic Science and Technology of ChinaQuzhouChina
- University of Electronic Science and Technology of ChinaChengduChina
| | - Haigang Gong
- Yangtze Delta Region Institute(Quzhou), University of Electronic Science and Technology of ChinaQuzhouChina
- University of Electronic Science and Technology of ChinaChengduChina
| | - Ming Liu
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's HospitalQuzhouChina
- University of Electronic Science and Technology of ChinaChengduChina
| | - Lifeng Xu
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's HospitalQuzhouChina
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Muller FM, Maebe J, Vanhove C, Vandenberghe S. Dose reduction and image enhancement in micro-CT using deep learning. Med Phys 2023; 50:5643-5656. [PMID: 36994779 DOI: 10.1002/mp.16385] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/14/2023] [Accepted: 03/09/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND In preclinical settings, micro-computed tomography (CT) provides a powerful tool to acquire high resolution anatomical images of rodents and offers the advantage to in vivo non-invasively assess disease progression and therapy efficacy. Much higher resolutions are needed to achieve scale-equivalent discriminatory capabilities in rodents as those in humans. High resolution imaging however comes at the expense of increased scan times and higher doses. Specifically, with preclinical longitudinal imaging, there are concerns that dose accumulation may affect experimental outcomes of animal models. PURPOSE Dose reduction efforts under the ALARA (as low as reasonably achievable) principles are thus a key point of attention. However, low dose CT acquisitions inherently induce higher noise levels which deteriorate image quality and negatively impact diagnostic performance. Many denoising techniques already exist, and deep learning (DL) has become increasingly popular for image denoising, but research has mostly focused on clinical CT with limited studies conducted on preclinical CT imaging. We investigate the potential of convolutional neural networks (CNN) for restoring high quality micro-CT images from low dose (noisy) images. The novelty of the CNN denoising frameworks presented in this work consists of utilizing image pairs with realistic CT noise present in the input as well as the target image used for the model training; a noisier image acquired with a low dose protocol is matched to a less noisy image acquired with a higher dose scan of the same mouse. METHODS Low and high dose ex vivo micro-CT scans of 38 mice were acquired. Two CNN models, based on a 2D and 3D four-layer U-Net, were trained with mean absolute error (30 training, 4 validation and 4 test sets). To assess denoising performance, ex vivo mice and phantom data were used. Both CNN approaches were compared to existing methods, like spatial filtering (Gaussian, Median, Wiener) and iterative total variation image reconstruction algorithm. Image quality metrics were derived from the phantom images. A first observer study (n = 23) was set-up to rank overall quality of differently denoised images. A second observer study (n = 18) estimated the dose reduction factor of the investigated 2D CNN method. RESULTS Visual and quantitative results show that both CNN algorithms exhibit superior performance in terms of noise suppression, structural preservation and contrast enhancement over comparator methods. The quality scoring by 23 medical imaging experts also indicates that the investigated 2D CNN approach is consistently evaluated as the best performing denoising method. Results from the second observer study and quantitative measurements suggest that CNN-based denoising could offer a 2-4× dose reduction, with an estimated dose reduction factor of about 3.2 for the considered 2D network. CONCLUSIONS Our results demonstrate the potential of DL in micro-CT for higher quality imaging at low dose acquisition settings. In the context of preclinical research, this offers promising future prospects for managing the cumulative severity effects of radiation in longitudinal studies.
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Affiliation(s)
- Florence M Muller
- Medical Image and Signal Processing (MEDISIP), Department of Electronics and Information Systems, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Jens Maebe
- Medical Image and Signal Processing (MEDISIP), Department of Electronics and Information Systems, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Christian Vanhove
- Medical Image and Signal Processing (MEDISIP), Department of Electronics and Information Systems, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
| | - Stefaan Vandenberghe
- Medical Image and Signal Processing (MEDISIP), Department of Electronics and Information Systems, Faculty of Engineering and Architecture, Ghent University, Ghent, Belgium
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12
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Wang J, Tang Y, Wu Z, Du Q, Yao L, Yang X, Li M, Zheng J. A self-supervised guided knowledge distillation framework for unpaired low-dose CT image denoising. Comput Med Imaging Graph 2023; 107:102237. [PMID: 37116340 DOI: 10.1016/j.compmedimag.2023.102237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/21/2023] [Accepted: 04/13/2023] [Indexed: 04/30/2023]
Abstract
Low-dose computed tomography (LDCT) can significantly reduce the damage of X-ray to the human body, but the reduction of CT dose will produce images with severe noise and artifacts, which will affect the diagnosis of doctors. Recently, deep learning has attracted more and more attention from researchers. However, most of the denoising networks applied to deep learning-based LDCT imaging are supervised methods, which require paired data for network training. In a realistic imaging scenario, obtaining well-aligned image pairs is challenging due to the error in the table re-positioning and the patient's physiological movement during data acquisition. In contrast, the unpaired learning method can overcome the drawbacks of supervised learning, making it more feasible to collect unpaired training data in most real-world imaging applications. In this study, we develop a novel unpaired learning framework, Self-Supervised Guided Knowledge Distillation (SGKD), which enables the guidance of supervised learning using the results generated by self-supervised learning. The proposed SGKD scheme contains two stages of network training. First, we can achieve the LDCT image quality improvement by the designed self-supervised cycle network. Meanwhile, it can also produce two complementary training datasets from the unpaired LDCT and NDCT images. Second, a knowledge distillation strategy with the above two datasets is exploited to further improve the LDCT image denoising performance. To evaluate the effectiveness and feasibility of the proposed method, extensive experiments were performed on the simulated AAPM challenging and real-world clinical LDCT datasets. The qualitative and quantitative results show that the proposed SGKD achieves better performance in terms of noise suppression and detail preservation compared with some state-of-the-art network models.
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Affiliation(s)
- Jiping Wang
- Institute of Electronic Information Engineering, Changchun University of Science and Technology, Changchun 130022, China; Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yufei Tang
- Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Zhongyi Wu
- Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Qiang Du
- Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Libing Yao
- Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Xiaodong Yang
- Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Ming Li
- Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
| | - Jian Zheng
- Institute of Electronic Information Engineering, Changchun University of Science and Technology, Changchun 130022, China; Medical Imaging Department, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
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13
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Yang S, Pu Q, Lei C, Zhang Q, Jeon S, Yang X. Low-dose CT denoising with a high-level feature refinement and dynamic convolution network. Med Phys 2022. [PMID: 36542402 DOI: 10.1002/mp.16175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/31/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Since the potential health risks of the radiation generated by computer tomography (CT), concerns have been expressed on reducing the radiation dose. However, low-dose CT (LDCT) images contain complex noise and artifacts, bringing uncertainty to medical diagnosis. PURPOSE Existing deep learning (DL)-based denoising methods are difficult to fully exploit hierarchical features of different levels, limiting the effect of denoising. Moreover, the standard convolution kernel is parameter sharing and cannot be adjusted dynamically with input change. This paper proposes an LDCT denoising network using high-level feature refinement and multiscale dynamic convolution to mitigate these problems. METHODS The dual network structure proposed in this paper consists of the feature refinement network (FRN) and the dynamic perception network (DPN). The FDN extracts features of different levels through residual dense connections. The high-level hierarchical information is transmitted to DPN to improve the low-level representations. In DPN, the two networks' features are fused by local channel attention (LCA) to assign weights in different regions and handle CT images' delicate tissues better. Then, the dynamic dilated convolution (DDC) with multibranch and multiscale receptive fields is proposed to enhance the expression and processing ability of the denoising network. The experiments were trained and tested on the dataset "NIH-AAPM-Mayo Clinic Low-Dose CT Grand Challenge," consisting of 10 anonymous patients with normal-dose abdominal CT and LDCT at 25% dose. In addition, external validation was performed on the dataset "Low Dose CT Image and Projection Data," which included 300 chest CT images at 10% dose and 300 head CT images at 25% dose. RESULTS Proposed method compared with seven mainstream LDCT denoising algorithms. On the Mayo dataset, achieved peak signal-to-noise ratio (PSNR): 46.3526 dB (95% CI: 46.0121-46.6931 dB) and structural similarity (SSIM): 0.9844 (95% CI: 0.9834-0.9854). Compared with LDCT, the average increase was 3.4159 dB and 0.0239, respectively. The results are relatively optimal and statistically significant compared with other methods. In external verification, our algorithm can cope well with ultra-low-dose chest CT images at 10% dose and obtain PSNR: 28.6130 (95% CI: 28.1680-29.0580 dB) and SSIM: 0.7201 (95% CI: 0.7101-0.7301). Compared with LDCT, PSNR/SSIM is increased by 3.6536dB and 0.2132, respectively. In addition, the quality of LDCT can also be improved in head CT denoising. CONCLUSIONS This paper proposes a DL-based LDCT denoising algorithm, which utilizes high-level features and multiscale dynamic convolution to optimize the network's denoising effect. This method can realize speedy denoising and performs well in noise suppression and detail preservation, which can be helpful for the diagnosis of LDCT.
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Affiliation(s)
- Sihan Yang
- College of Electronics and Information Engineering, Sichuan University, Chengdu, Sichuan, China.,School of Aeronautics and Astronautics, Sichuan University, Chengdu, Sichuan, China
| | - Qiang Pu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chunting Lei
- College of Electronics and Information Engineering, Sichuan University, Chengdu, Sichuan, China.,School of Aeronautics and Astronautics, Sichuan University, Chengdu, Sichuan, China
| | - Qiao Zhang
- Macro Net Communication Co., Ltd., Chongqing, China
| | - Seunggil Jeon
- Samsung Electronics, Suwon-si, Gyeonggi-do, Republic of Korea
| | - Xiaomin Yang
- College of Electronics and Information Engineering, Sichuan University, Chengdu, Sichuan, China.,School of Aeronautics and Astronautics, Sichuan University, Chengdu, Sichuan, China
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14
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Zhu M, Mao Z, Li D, Wang Y, Zeng D, Bian Z, Ma J. Structure-preserved meta-learning uniting network for improving low-dose CT quality. Phys Med Biol 2022; 67. [PMID: 36351294 DOI: 10.1088/1361-6560/aca194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/09/2022] [Indexed: 11/10/2022]
Abstract
Objective.Deep neural network (DNN) based methods have shown promising performances for low-dose computed tomography (LDCT) imaging. However, most of the DNN-based methods are trained on simulated labeled datasets, and the low-dose simulation algorithms are usually designed based on simple statistical models which deviate from the real clinical scenarios, which could lead to issues of overfitting, instability and poor robustness. To address these issues, in this work, we present a structure-preserved meta-learning uniting network (shorten as 'SMU-Net') to suppress noise-induced artifacts and preserve structure details in the unlabeled LDCT imaging task in real scenarios.Approach.Specifically, the presented SMU-Net contains two networks, i.e., teacher network and student network. The teacher network is trained on simulated labeled dataset and then helps the student network train with the unlabeled LDCT images via the meta-learning strategy. The student network is trained on real LDCT dataset with the pseudo-labels generated by the teacher network. Moreover, the student network adopts the Co-teaching strategy to improve the robustness of the presented SMU-Net.Main results.We validate the proposed SMU-Net method on three public datasets and one real low-dose dataset. The visual image results indicate that the proposed SMU-Net has superior performance on reducing noise-induced artifacts and preserving structure details. And the quantitative results exhibit that the presented SMU-Net method generally obtains the highest signal-to-noise ratio (PSNR), the highest structural similarity index measurement (SSIM), and the lowest root-mean-square error (RMSE) values or the lowest natural image quality evaluator (NIQE) scores.Significance.We propose a meta learning strategy to obtain high-quality CT images in the LDCT imaging task, which is designed to take advantage of unlabeled CT images to promote the reconstruction performance in the LDCT environments.
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Affiliation(s)
- Manman Zhu
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Zerui Mao
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Danyang Li
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Yongbo Wang
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Dong Zeng
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Zhaoying Bian
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Jianhua Ma
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, People's Republic of China
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15
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Kim W, Lee J, Kang M, Kim JS, Choi JH. Wavelet subband-specific learning for low-dose computed tomography denoising. PLoS One 2022; 17:e0274308. [PMID: 36084002 PMCID: PMC9462582 DOI: 10.1371/journal.pone.0274308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/25/2022] [Indexed: 11/19/2022] Open
Abstract
Deep neural networks have shown great improvements in low-dose computed tomography (CT) denoising. Early algorithms were primarily optimized to obtain an accurate image with low distortion between the denoised image and reference full-dose image at the cost of yielding an overly smoothed unrealistic CT image. Recent research has sought to preserve the fine details of denoised images with high perceptual quality, which has been accompanied by a decrease in objective quality due to a trade-off between perceptual quality and distortion. We pursue a network that can generate accurate and realistic CT images with high objective and perceptual quality within one network, achieving a better perception-distortion trade-off. To achieve this goal, we propose a stationary wavelet transform-assisted network employing the characteristics of high- and low-frequency domains of the wavelet transform and frequency subband-specific losses defined in the wavelet domain. We first introduce a stationary wavelet transform for the network training procedure. Then, we train the network using objective loss functions defined for high- and low-frequency domains to enhance the objective quality of the denoised CT image. With this network design, we train the network again after replacing the objective loss functions with perceptual loss functions in high- and low-frequency domains. As a result, we acquired denoised CT images with high perceptual quality using this strategy while minimizing the objective quality loss. We evaluated our algorithms on the phantom and clinical images, and the quantitative and qualitative results indicate that ours outperform the existing state-of-the-art algorithms in terms of objective and perceptual quality.
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Affiliation(s)
- Wonjin Kim
- Division of Mechanical and Biomedical Engineering, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Jaayeon Lee
- Division of Mechanical and Biomedical Engineering, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
| | - Mihyun Kang
- Department of Cyber Security, Ewha Womans University, Seoul, Republic of Korea
| | - Jin Sung Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jang-Hwan Choi
- Division of Mechanical and Biomedical Engineering, Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea
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16
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Liu J, Jiang H, Ning F, Li M, Pang W. DFSNE-Net: Deviant feature sensitive noise estimate network for low-dose CT denoising. Comput Biol Med 2022; 149:106061. [DOI: 10.1016/j.compbiomed.2022.106061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/10/2022] [Accepted: 08/27/2022] [Indexed: 11/26/2022]
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17
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Zhang Z, Liang X, Zhao W, Xing L. Noise2Context: Context-assisted learning 3D thin-layer for low-dose CT. Med Phys 2021; 48:5794-5803. [PMID: 34287948 DOI: 10.1002/mp.15119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/31/2021] [Accepted: 07/08/2021] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Computed tomography (CT) has played a vital role in medical diagnosis, assessment, and therapy planning, etc. In clinical practice, concerns about the increase of x-ray radiation exposure attract more and more attention. To lower the x-ray radiation, low-dose CT (LDCT) has been widely adopted in certain scenarios, while it will induce the degradation of CT image quality. In this paper, we proposed a deep learning-based method that can train denoising neural networks without any clean data. METHODS In this work, for 3D thin-slice LDCT scanning, we first drive an unsupervised loss function which was equivalent to a supervised loss function with paired noisy and clean samples when the noise in the different slices from a single scan was uncorrelated and zero-mean. Then, we trained the denoising neural network to map one noise LDCT image to its two adjacent LDCT images in a single 3D thin-layer LDCT scanning, simultaneously. In essence, with some latent assumptions, we proposed an unsupervised loss function to train the denoising neural network in an unsupervised manner, which integrated the similarity between adjacent CT slices in 3D thin-layer LDCT. RESULTS Further experiments on Mayo LDCT dataset and a realistic pig head were carried out. In the experiments using Mayo LDCT dataset, our unsupervised method can obtain performance comparable to that of the supervised baseline. With the realistic pig head, our method can achieve optimal performance at different noise levels as compared to all the other methods that demonstrated the superiority and robustness of the proposed Noise2Context. CONCLUSIONS In this work, we present a generalizable LDCT image denoising method without any clean data. As a result, our method not only gets rid of the complex artificial image priors but also amounts of paired high-quality training datasets.
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Affiliation(s)
- Zhicheng Zhang
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Xiaokun Liang
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Wei Zhao
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Lei Xing
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
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