Parameter optimization for local polynomial approximation based intersection confidence interval filter using genetic algorithm: an application for brain MRI image de-noising

Magnetic resonance imaging (MRI) is extensively exploited for more accuratepathological changes as well as diagnosis. Conversely, MRI suffers from variousshortcomings such as ambient noise from the environment, acquisition noise from theequipment, the presence of background tissue, breathing motion, body fat, etc.Consequently, noise reduction is critical as diverse types of the generated noise limit the efficiency of the medical image diagnosis. Local polynomial approximation basedintersection confidence interval (LPA-ICI) filter is one of the effective de-noising filters.This filter requires an adjustment of the ICI parameters for efficient window size selection.From the wide range of ICI parametric values, finding out the best set of tunes values is itselfan optimization problem. The present study proposed a novel technique for parameteroptimization of LPA-ICI filter using genetic algorithm (GA) for brain MR imagesde-noising. The experimental results proved that the proposed method outperforms theLPA-ICI method for de-noising in terms of various performance metrics for different noisevariance levels. Obtained results reports that the ICI parameter values depend on the noisevariance and the concerned under test image

Real-time Ultrasound Signals Processing: Denoising and Super-resolution

Ultrasound acquisition is widespread in the biomedical field, due to its properties of low cost, portability, and non-invasiveness for the patient. The processing and analysis of US signals, such as images, 2D videos, and volumetric images, allows the physician to monitor the evolution of the patient's disease, and support diagnosis, and treatments (e.g., surgery). US images are affected by speckle noise, generated by the overlap of US waves. Furthermore, low-resolution images are acquired when a high acquisition frequency is applied to accurately characterise the behaviour of anatomical features that quickly change over time. Denoising and super-resolution of US signals are relevant to improve the visual evaluation of the physician and the performance and accuracy of processing methods, such as segmentation and classification. The main requirements for the processing and analysis of US signals are real-time execution, preservation of anatomical features, and reduction of artefacts. In this context, we present a novel framework for the real-time denoising of US 2D images based on deep learning and high-performance computing, which reduces noise while preserving anatomical features in real-time execution. We extend our framework to the denoise of arbitrary US signals, such as 2D videos and 3D images, and we apply denoising algorithms that account for spatio-temporal signal properties into an image-to-image deep learning model. As a building block of this framework, we propose a novel denoising method belonging to the class of low-rank approximations, which learns and predicts the optimal thresholds of the Singular Value Decomposition. While previous denoise work compromises the computational cost and effectiveness of the method, the proposed framework achieves the results of the best denoising algorithms in terms of noise removal, anatomical feature preservation, and geometric and texture properties conservation, in a real-time execution that respects industrial constraints. The framework reduces the artefacts (e.g., blurring) and preserves the spatio-temporal consistency among frames/slices; also, it is general to the denoising algorithm, anatomical district, and noise intensity. Then, we introduce a novel framework for the real-time reconstruction of the non-acquired scan lines through an interpolating method; a deep learning model improves the results of the interpolation to match the target image (i.e., the high-resolution image). We improve the accuracy of the prediction of the reconstructed lines through the design of the network architecture and the loss function. %The design of the deep learning architecture and the loss function allow the network to improve the accuracy of the prediction of the reconstructed lines. In the context of signal approximation, we introduce our kernel-based sampling method for the reconstruction of 2D and 3D signals defined on regular and irregular grids, with an application to US 2D and 3D images. Our method improves previous work in terms of sampling quality, approximation accuracy, and geometry reconstruction with a slightly higher computational cost. For both denoising and super-resolution, we evaluate the compliance with the real-time requirement of US applications in the medical domain and provide a quantitative evaluation of denoising and super-resolution methods on US and synthetic images. Finally, we discuss the role of denoising and super-resolution as pre-processing steps for segmentation and predictive analysis of breast pathologies

Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

Mumford-Shah and Potts Regularization for Manifold-Valued Data with Applications to DTI and Q-Ball Imaging

Mumford-Shah and Potts functionals are powerful variational models for regularization which are widely used in signal and image processing; typical applications are edge-preserving denoising and segmentation. Being both non-smooth and non-convex, they are computationally challenging even for scalar data. For manifold-valued data, the problem becomes even more involved since typical features of vector spaces are not available. In this paper, we propose algorithms for Mumford-Shah and for Potts regularization of manifold-valued signals and images. For the univariate problems, we derive solvers based on dynamic programming combined with (convex) optimization techniques for manifold-valued data. For the class of Cartan-Hadamard manifolds (which includes the data space in diffusion tensor imaging), we show that our algorithms compute global minimizers for any starting point. For the multivariate Mumford-Shah and Potts problems (for image regularization) we propose a splitting into suitable subproblems which we can solve exactly using the techniques developed for the corresponding univariate problems. Our method does not require any a priori restrictions on the edge set and we do not have to discretize the data space. We apply our method to diffusion tensor imaging (DTI) as well as Q-ball imaging. Using the DTI model, we obtain a segmentation of the corpus callosum

Diffusion Models for Medical Image Analysis: A Comprehensive Survey

Denoising diffusion models, a class of generative models, have garnered immense interest lately in various deep-learning problems. A diffusion probabilistic model defines a forward diffusion stage where the input data is gradually perturbed over several steps by adding Gaussian noise and then learns to reverse the diffusion process to retrieve the desired noise-free data from noisy data samples. Diffusion models are widely appreciated for their strong mode coverage and quality of the generated samples despite their known computational burdens. Capitalizing on the advances in computer vision, the field of medical imaging has also observed a growing interest in diffusion models. To help the researcher navigate this profusion, this survey intends to provide a comprehensive overview of diffusion models in the discipline of medical image analysis. Specifically, we introduce the solid theoretical foundation and fundamental concepts behind diffusion models and the three generic diffusion modelling frameworks: diffusion probabilistic models, noise-conditioned score networks, and stochastic differential equations. Then, we provide a systematic taxonomy of diffusion models in the medical domain and propose a multi-perspective categorization based on their application, imaging modality, organ of interest, and algorithms. To this end, we cover extensive applications of diffusion models in the medical domain. Furthermore, we emphasize the practical use case of some selected approaches, and then we discuss the limitations of the diffusion models in the medical domain and propose several directions to fulfill the demands of this field. Finally, we gather the overviewed studies with their available open-source implementations at https://github.com/amirhossein-kz/Awesome-Diffusion-Models-in-Medical-Imaging.Comment: Second revision: including more papers and further discussion

Accelerated High-Resolution Photoacoustic Tomography via Compressed Sensing

Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue. A particular example is the planar Fabry-Perot (FP) scanner, which yields high-resolution images but takes several minutes to sequentially map the photoacoustic field on the sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant. We demonstrate that combining variational image reconstruction methods using spatial sparsity constraints with the development of novel PAT acquisition systems capable of sub-sampling the acoustic wave field can dramatically increase the acquisition speed while maintaining a good spatial resolution: First, we describe and model two general spatial sub-sampling schemes. Then, we discuss how to implement them using the FP scanner and demonstrate the potential of these novel compressed sensing PAT devices through simulated data from a realistic numerical phantom and through measured data from a dynamic experimental phantom as well as from in-vivo experiments. Our results show that images with good spatial resolution and contrast can be obtained from highly sub-sampled PAT data if variational image reconstruction methods that describe the tissues structures with suitable sparsity-constraints are used. In particular, we examine the use of total variation regularization enhanced by Bregman iterations. These novel reconstruction strategies offer new opportunities to dramatically increase the acquisition speed of PAT scanners that employ point-by-point sequential scanning as well as reducing the channel count of parallelized schemes that use detector arrays.Comment: submitted to "Physics in Medicine and Biology

BRUISE DETECTION IN APPLES USING 3D INFRARED IMAGING AND MACHINE LEARNING TECHNOLOGIES

Bruise detection plays an important role in fruit grading. A bruise detection system capable of finding and removing damaged products on the production lines will distinctly improve the quality of fruits for sale, and consequently improve the fruit economy. This dissertation presents a novel automatic detection system based on surface information obtained from 3D near-infrared imaging technique for bruised apple identification. The proposed 3D bruise detection system is expected to provide better performance in bruise detection than the existing 2D systems. We first propose a mesh denoising filter to reduce noise effect while preserving the geometric features of the meshes. Compared with several existing mesh denoising filters, the proposed filter achieves better performance in reducing noise effect as well as preserving bruised regions in 3D meshes of bruised apples. Next, we investigate two different machine learning techniques for the identification of bruised apples. The first technique is to extract hand-crafted feature from 3D meshes, and train a predictive classifier based on hand-crafted features. It is shown that the predictive model trained on the proposed hand-crafted features outperforms the same models trained on several other local shape descriptors. The second technique is to apply deep learning to learn the feature representation automatically from the mesh data, and then use the deep learning model or a new predictive model for the classification. The optimized deep learning model achieves very high classification accuracy, and it outperforms the performance of the detection system based on the proposed hand-crafted features. At last, we investigate GPU techniques for accelerating the proposed apple bruise detection system. Specifically, the dissertation proposes a GPU framework, implemented in CUDA, for the acceleration of the algorithm that extracts vertex-based local binary patterns. Experimental results show that the proposed GPU program speeds up the process of extracting local binary patterns by 5 times compared to a single-core CPU program

A Review on MR Image Intensity Inhomogeneity Correction

Intensity inhomogeneity (IIH) is often encountered in MR imaging, and a number of techniques have been devised to correct this artifact. This paper attempts to review some of the recent developments in the mathematical modeling of IIH field. Low-frequency models are widely used, but they tend to corrupt the low-frequency components of the tissue. Hypersurface models and statistical models can be adaptive to the image and generally more stable, but they are also generally more complex and consume more computer memory and CPU time. They are often formulated together with image segmentation within one framework and the overall performance is highly dependent on the segmentation process. Beside these three popular models, this paper also summarizes other techniques based on different principles. In addition, the issue of quantitative evaluation and comparative study are discussed