Uncertainty quantification in inverse medical imaging tasks with deep learning has received little attention. However, deep models trained on large data sets tend to hallucinate and create artifacts in the reconstructed output that are not anatomically present. We use a randomly initialized convolutional network as parameterization of the reconstructed image and perform gradient descent to match the observation, which is known as deep image prior. In this case, the reconstruction does not suffer from hallucinations as no prior training is performed. We extend this to a Bayesian approach with Monte Carlo dropout to quantify both aleatoric and epistemic uncertainty. The presented method is evaluated on the task of denoising different medical imaging modalities. The experimental results show that our approach yields well-calibrated uncertainty. That is, the predictive uncertainty correlates with the predictive error. This allows for reliable uncertainty estimates and can tackle the problem of hallucinations and artifacts in inverse medical imaging tasks.
Birla Institute of Technology Science Pilani（比尔拉理工学院皮拉尼分校）
In this work, we present Eformer - Edge enhancement based transformer, a novel architecture that builds an encoder-decoder network using transformer blocks for medical image denoising. Non-overlapping window-based self-attention is used in the transformer block that reduces computational requirements. This work further incorporates learnable Sobel-Feldman operators to enhance edges in the image and propose an effective way to concatenate them in the intermediate layers of our architecture. The experimental analysis is conducted by comparing deterministic learning and residual learning for the …
Task-based Regularization in Penalized Least-Squares for Binary Signal Detection Tasks in Medical Image Denoising
University of Michigan-Shanghai Jiao Tong University Joint Institute（密歇根大学-上海交通大学联合研究院）；Global Institute of Future Technology, Shanghai Jiao Tong University（上海交通大学未来科技全球研究院）；Wyant College of Optical Sciences, University of Arizona（亚利桑那大学怀恩特光学科学学院）；Department of Medical Imaging, University of Arizona（亚利桑那大学医学影像系）
School of Computer and Communication Sciences, EPFL（洛桑联邦理工学院计算机与通信科学学院）
Blind and universal image denoising consists of using a unique model that denoises images with any level of noise. It is especially practical as noise levels do not need to be known when the model is developed or at test time. We propose a theoretically-grounded blind and universal deep learning image denoiser for additive Gaussian noise removal. Our network is based on an optimal denoising solution, which we call fusion denoising. It is derived theoretically with a Gaussian image prior assumption. Synthetic experiments show our network's generalization strength to unseen additive noise levels…
The extensive use of medical CT has raised a public concern over the radiation dose to the patient. Reducing the radiation dose leads to increased CT image noise and artifacts, which can adversely affect not only the radiologists judgement but also the performance of downstream medical image analysis tasks. Various low-dose CT denoising methods, especially the recent deep learning based approaches, have produced impressive results. However, the existing denoising methods are all downstream-task-agnostic and neglect the diverse needs of the downstream applications. In this paper, we introduce a…
In this paper, we consider Bayesian image denoising based on a Gaussian Markov random field (GMRF) model, for which we propose an new algorithm. Our method can solve Bayesian image denoising problems, including hyperparameter estimation, in $O(n)$-time, where $n$ is the number of pixels in a given image. From the perspective of the order of the computational time, this is a state-of-the-art algorithm for the present problem setting. Moreover, the results of our numerical experiments we show our method is in fact effective in practice.
Natural images are often affected by random noise and image denoising has long been a central topic in Computer Vision. Many algorithms have been introduced to remove the noise from the natural images, such as Gaussian, Wiener filtering and wavelet thresholding. However, many of these algorithms remove the fine edges and make them blur. Recently, many promising denoising algorithms have been introduced such as Non-local Means, Fields of Experts, and BM3D. In this paper, we explore Bayesian method of ensemble learning for image denoising. Ensemble methods seek to combine multiple different algo…
Duke University（杜克大学）；Télécom ParisTech, Université Paris-Saclay（巴黎高科电信学院，巴黎-萨克雷大学）；Université Paris Descartes（巴黎笛卡尔大学）；Universidad de la República（共和国大学）
Recently, impressive denoising results have been achieved by Bayesian approaches which assume Gaussian models for the image patches. This improvement in performance can be attributed to the use of per-patch models. Unfortunately such an approach is particularly unstable for most inverse problems beyond denoising. In this work, we propose the use of a hyperprior to model image patches, in order to stabilize the estimation procedure. There are two main advantages to the proposed restoration scheme: Firstly it is adapted to diagonal degradation matrices, and in particular to missing data problems…
Regularization by denoising: Bayesian model and Langevin-within-split Gibbs sampling
Institut Denis Poisson, University of Orléans（德尼·泊松研究所，奥尔良大学）；University of Toulouse, IRIT/INP-ENSEEIHT, CNRS（图卢兹大学，法国国家信息与自动化研究所/国立高等电子、电子技术、计算机与机械学院，法国国家科学研究中心）
本文提出一种基于去噪正则化（RED）的图像反演贝叶斯框架，并设计了内含Langevin Monte Carlo步骤的分裂Gibbs采样算法，通过去模糊等任务验证了其有效性。
Image restoration has been an extensively researched topic in numerous fields. With the advent of deep learning, a lot of the current algorithms were replaced by algorithms that are more flexible and robust. Deep networks have demonstrated impressive performance in a variety of tasks like blind denoising, image enhancement, deblurring, super-resolution, inpainting, among others. Most of these learning-based algorithms use a large amount of clean data during the training process. However, in certain applications in medical image processing, one may not have access to a large amount of clean dat…
Harbin Institute of Technology（哈尔滨工业大学）；Megvii Inc（旷视科技有限公司）
Recently, deep learning-based image denoising methods have achieved promising performance on test data with the same distribution as training set, where various denoising models based on synthetic or collected real-world training data have been learned. However, when handling real-world noisy images, the denoising performance is still limited. In this paper, we propose a simple yet effective Bayesian deep ensemble (BDE) method for real-world image denoising, where several representative deep denoisers pre-trained with various training data settings can be fused to improve robustness. The found…
Image denoising is a typical ill-posed problem due to complex degradation. Leading methods based on normalizing flows have tried to solve this problem with an invertible transformation instead of a deterministic mapping. However, the implicit bijective mapping is not explored well. Inspired by a latent observation that noise tends to appear in the high-frequency part of the image, we propose a fully invertible denoising method that injects the idea of disentangled learning into a general invertible neural network to split noise from the high-frequency part. More specifically, we decompose the …
University of California at San Diego（加州大学圣地亚哥分校）；Purdue University（普渡大学）
We propose a data-dependent denoising procedure to restore noisy images. Different from existing denoising algorithms which search for patches from either the noisy image or a generic database, the new algorithm finds patches from a database that contains only relevant patches. We formulate the denoising problem as an optimal filter design problem and make two contributions. First, we determine the basis function of the denoising filter by solving a group sparsity minimization problem. The optimization formulation generalizes existing denoising algorithms and offers systematic analysis of the …
Natural image statistics exhibit hierarchical dependencies across multiple scales. Representing such prior knowledge in non-factorial latent tree models can boost performance of image denoising, inpainting, deconvolution or reconstruction substantially, beyond standard factorial "sparse" methodology. We derive a large scale approximate Bayesian inference algorithm for linear models with non-factorial (latent tree-structured) scale mixture priors. Experimental results on a range of denoising and inpainting problems demonstrate substantially improved performance compared to MAP estimation or to …
Image denoising is an essential part of many image processing and computer vision tasks due to inevitable noise corruption during image acquisition. Traditionally, many researchers have investigated image priors for the denoising, within the Bayesian perspective based on image properties and statistics. Recently, deep convolutional neural networks (CNNs) have shown great success in image denoising by incorporating large-scale synthetic datasets. However, they both have pros and cons. While the deep CNNs are powerful for removing the noise with known statistics, they tend to lack flexibility an…
Structure-Adaptive Sparse Diffusion in Voxel Space for 3D Medical Image Enhancement
Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA（佛罗里达大学电气与计算机工程系）；Department of Medicine, University of Florida, Gainesville, FL, USA（佛罗里达大学医学系）；Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA（佛罗里达大学生物医学工程系）；Research Computing, University of Florida, Gainesville, FL, USA（佛罗里达大学研究计算中心）；NVIDIA, Santa Clara, CA, USA（英伟达）
With the advent of advances in self-supervised learning, paired clean-noisy data are no longer required in deep learning-based image denoising. However, existing blind denoising methods still require the assumption with regard to noise characteristics, such as zero-mean noise distribution and pixel-wise noise-signal independence; this hinders wide adaptation of the method in the medical domain. On the other hand, unpaired learning can overcome limitations related to the assumption on noise characteristics, which makes it more feasible for collecting the training data in real-world scenarios. I…
Peking University（北京大学）；Academy for Advanced Interdisciplinary Studies（前沿交叉学科研究院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
We propose a novel and unified method, measurement-conditioned denoising diffusion probabilistic model (MC-DDPM), for under-sampled medical image reconstruction based on DDPM. Different from previous works, MC-DDPM is defined in measurement domain (e.g. k-space in MRI reconstruction) and conditioned on under-sampling mask. We apply this method to accelerate MRI reconstruction and the experimental results show excellent performance, outperforming full supervision baseline and the state-of-the-art score-based reconstruction method. Due to its generative nature, MC-DDPM can also quantify the unce…
In this paper, we propose a new image denoising method, tailored to specific classes of images, assuming that a dataset of clean images of the same class is available. Similarly to the non-local means (NLM) algorithm, the proposed method computes a weighted average of non-local patches, which we interpret under the importance sampling framework. This viewpoint introduces flexibility regarding the adopted priors, the noise statistics, and the computation of Bayesian estimates. The importance sampling viewpoint is exploited to approximate the minimum mean squared error (MMSE) patch estimates, us…
Image denoising is of great importance for medical imaging system, since it can improve image quality for disease diagnosis and downstream image analyses. In a variety of applications, dynamic imaging techniques are utilized to capture the time-varying features of the subject, where multiple images are acquired for the same subject at different time points. Although signal-to-noise ratio of each time frame is usually limited by the short acquisition time, the correlation among different time frames can be exploited to improve denoising results with shared information across time frames. With t…
A successful class of image denoising methods is based on Bayesian approaches working in wavelet representations. However, analytical estimates can be obtained only for particular combinations of analytical models of signal and noise, thus precluding its straightforward extension to deal with other arbitrary noise sources. In this paper, we propose an alternative non-explicit way to take into account the relations among natural image wavelet coefficients for denoising: we use support vector regression (SVR) in the wavelet domain to enforce these relations in the estimated signal. Since relatio…
University of California at San Diego（加利福尼亚大学圣迭戈分校）；Purdue University（普渡大学）
We propose an adaptive learning procedure to learn patch-based image priors for image denoising. The new algorithm, called the Expectation-Maximization (EM) adaptation, takes a generic prior learned from a generic external database and adapts it to the noisy image to generate a specific prior. Different from existing methods that combine internal and external statistics in ad-hoc ways, the proposed algorithm is rigorously derived from a Bayesian hyper-prior perspective. There are two contributions of this paper: First, we provide full derivation of the EM adaptation algorithm and demonstrate m…
Confocal microscopy is essential for histopathologic cell visualization and quantification. Despite its significant role in biology, fluorescence confocal microscopy suffers from the presence of inherent noise during image acquisition. Non-local patch-wise Bayesian mean filtering (NLB) was until recently the state-of-the-art denoising approach. However, classic denoising methods have been outperformed by neural networks in recent years. In this work, we propose to exploit the strengths of NLB in the framework of Bayesian deep learning. We do so by designing a convolutional neural network and t…
We cast the problem of image denoising as a domain translation problem between high and low noise domains. By modifying the cycleGAN model, we are able to learn a mapping between these domains on unpaired retinal optical coherence tomography images. In quantitative measurements and a qualitative evaluation by ophthalmologists, we show how this approach outperforms other established methods. The results indicate that the network differentiates subtle changes in the level of noise in the image. Further investigation of the model's feature maps reveals that it has learned to distinguish retinal l…
National Tsing Hua University（国立清华大学）；Florida International University（佛罗里达国际大学）；Lehigh University（理海大学）；Guangdong Provincial People’s Hospital（广东省人民医院）；Guangdong Academy of Medical Science（广东省医学科学院）；University of Notre Dame（圣母大学）
Deep learning had already demonstrated its power in medical images, including denoising, classification, segmentation, etc. All these applications are proposed to automatically analyze medical images beforehand, which brings more information to radiologists during clinical assessment for accuracy improvement. Recently, many medical denoising methods had shown their significant artifact reduction result and noise removal both quantitatively and qualitatively. However, those existing methods are developed around human-vision, i.e., they are designed to minimize the noise effect that can be perce…
Denoising Diffusion Models for Anomaly Localization in Medical Images
School of Computation, Information and Technology, Technical University of Munich（慕尼黑技术大学计算、信息与技术学院）；Institute of Machine Learning in Biomedical Imaging, Helmholtz Munich, Germany（生物医学影像机器学习研究所，海德堡慕尼黑德国）；Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland（巴塞尔大学生物医学工程系，瑞士Allschwil）；School of Biomedical Engineering and Imaging Sciences, King’s College London, United Kingdom（伦敦国王学院生物医学工程与影像科学学院，英国）；Department of Biomedical Informatics and Data Science, Yale University School of Medicine, New Haven, CT, USA（耶鲁大学医学院生物医学信息学与数据科学系，美国新罕布什尔州新 Haven）；Yale Biomedical Imaging Institute, Yale University, New Haven, CT, USA（耶鲁大学生物医学影像研究院，美国新罕布什尔州新 Haven）
Deep convolutional neural networks (DCNNs) have contributed many breakthroughs in segmentation tasks, especially in the field of medical imaging. However, \textit{domain shift} and \textit{corrupted annotations}, which are two common problems in medical imaging, dramatically degrade the performance of DCNNs in practice. In this paper, we propose a novel robust cross-denoising framework using two peer networks to address domain shift and corrupted label problems with a peer-review strategy. Specifically, each network performs as a mentor, mutually supervised to learn from reliable samples selec…
Center for Advanced Medical Computing and Analysis, Massachusetts General Hospital and Harvard Medical School（麻省总医院与哈佛医学院高级医学计算与分析中心）；Gordon Center for Medical Imaging, Massachusetts General Hospital and Harvard Medical School（麻省总医院与哈佛医学院戈登医学成像中心）
Deep neural networks have been proved efficient for medical image denoising. Current training methods require both noisy and clean images. However, clean images cannot be acquired for many practical medical applications due to naturally noisy signal, such as dynamic imaging, spectral computed tomography, arterial spin labeling magnetic resonance imaging, etc. In this paper we proposed a training method which learned denoising neural networks from noisy training samples only. Training data in the acquisition domain was split to two subsets and the network was trained to map one noisy set to the…
University Hospital Aachen（亚琛大学医院）；RWTH Aachen University（亚琛工业大学）；Ocumeda AG（奥库梅达股份公司）；University Hospital Heidelberg（海德堡大学医院）；University Hospital Würzburg（维尔茨堡大学医院）；University of Mainz（美因茨大学）；RWTH Aachen（亚琛工业大学）
Recent advances in computer vision have shown promising results in image generation. Diffusion probabilistic models in particular have generated realistic images from textual input, as demonstrated by DALL-E 2, Imagen and Stable Diffusion. However, their use in medicine, where image data typically comprises three-dimensional volumes, has not been systematically evaluated. Synthetic images may play a crucial role in privacy preserving artificial intelligence and can also be used to augment small datasets. Here we show that diffusion probabilistic models can synthesize high quality medical imagi…
RelativeFlow: Taming Medical Image Denoising Learning with Noisy Reference
School of Computer Science and Engineering, Southeast University, China（东南大学计算机科学与工程学院，中国）；Department of Biomedical Engineering, Case Western Reserve University, USA（凯斯西储大学生物医学工程系，美国）；School of Instrument Science and Engineering, Southeast University, China（东南大学仪器科学与工程学院，中国）；Department of Optical Sciences, University of Arizona, USA（亚利桑那大学光学科学系，美国）
In medical applications, weakly supervised anomaly detection methods are of great interest, as only image-level annotations are required for training. Current anomaly detection methods mainly rely on generative adversarial networks or autoencoder models. Those models are often complicated to train or have difficulties to preserve fine details in the image. We present a novel weakly supervised anomaly detection method based on denoising diffusion implicit models. We combine the deterministic iterative noising and denoising scheme with classifier guidance for image-to-image translation between d…
Canon Medical Research Europe（佳能医疗欧洲研究中心）；University of Glasgow（格拉斯哥大学）；University of Edinburgh（爱丁堡大学）；The Alan Turing Institute（艾伦·图灵研究所）
Pathological brain lesions exhibit diverse appearance in brain images, in terms of intensity, texture, shape, size, and location. Comprehensive sets of data and annotations are difficult to acquire. Therefore, unsupervised anomaly detection approaches have been proposed using only normal data for training, with the aim of detecting outlier anomalous voxels at test time. Denoising methods, for instance classical denoising autoencoders (DAEs) and more recently emerging diffusion models, are a promising approach, however naive application of pixelwise noise leads to poor anomaly detection perform…
Zhejiang University-University of Illinois Urbana-Champaign Institute（浙江大学-伊利诺伊大学厄巴纳-香槟分校联合学院）；Zhejiang University（浙江大学）
Reducing the radiation dose in computed tomography (CT) is important to mitigate radiation-induced risks. One option is to employ a well-trained model to compensate for incomplete information and map sparse-view measurements to the CT reconstruction. However, reconstruction from sparsely sampled measurements is insufficient to uniquely characterize an object in CT, and a learned prior model may be inadequate for unencountered cases. Medical modal translation from magnetic resonance imaging (MRI) to CT is an alternative but may introduce incorrect information into the synthesized CT images in a…
Indian Institute of Information Technology Vadodara（瓦多达拉印度信息技术学院）
Medical image acquisition is often intervented by unwanted noise that corrupts the information content. This paper introduces an unsupervised medical image denoising technique that learns noise characteristics from the available images and constructs denoised images. It comprises of two blocks of data processing, viz., patch-based dictionaries that indirectly learn the noise and residual learning (RL) that directly learns the noise. The model is generalized to account for both 2D and 3D images considering different medical imaging instruments. The images are considered one-by-one from the stac…
Wellcome Centre for Human Neuroimaging（惠康人类神经影像中心）；UCL（伦敦大学学院）；UCL Institute of Neurology（伦敦大学学院神经学研究所）
Automatically generating one medical imaging modality from another is known as medical image translation, and has numerous interesting applications. This paper presents an interpretable generative modelling approach to medical image translation. By allowing a common model for group-wise normalisation and segmentation of brain scans to handle missing data, the model allows for predicting entirely missing modalities from one, or a few, MR contrasts. Furthermore, the model can be trained on a fairly small number of subjects. The proposed model is validated on three clinically relevant scenarios. …
