Towards Computer Aided Management of Kidney Disease

Autosomal dominant polycystic kidney disease (ADPKD) is the fourth most common cause of kidney transplant worldwide accounting for 7-10% of all cases. Although ADPKD usually progresses over many decades, accurate risk prediction is an important task. Identifying patients with progressive disease is vital to providing new treatments being developed and enable them to enter clinical trials for new therapy. Among other factors, total kidney volume (TKV) is a major biomarker predicting the progression of ADPKD. Consortium for Radiologic Imaging Studies in Polycystic Kidney Disease (CRISP) have shown that TKV is an early, and accurate measure of cystic burden and likely growth rate. It is strongly associated with loss of renal function. While ultrasound (US) has proven as an excellent tool for diagnosing the disease; monitoring short-term changes using ultrasound has been shown to not be accurate. This is attributed to high operator variability and reproducibility as compared to tomographic modalities such as CT and MR (Gold standard). Ultrasound has emerged as one of the standout modalities for intra-procedural imaging and with methods for spatial localization has afforded us the ability to track 2D ultrasound in the physical space in which it is being used. In addition to this, the vast amount of recorded tomographic data can be used to generate statistical shape models that allow us to extract clinical value from archived image sets. Renal volumetry is of great interest in the management of chronic kidney diseases (CKD). In this work, we have implemented a tracked ultrasound system and developed a statistical shape model of the kidney. We utilize the tracked ultrasound to acquire a stack of slices that are able to capture the region of interest, in our case kidney phantoms, and reconstruct 3D volume from spatially localized 2D slices. Approximate shape data is then extracted from this 3D volume using manual segmentation of the organ and a shape model is fit to this data. This generates an instance from the shape model that best represents the scanned phantom and volume calculation is done on this instance. We observe that we can calculate the volume to within 10% error in estimation when compared to the gold standard volume of the phantom

A Deep Learning Approach to Denoise Optical Coherence Tomography Images of the Optic Nerve Head

Purpose: To develop a deep learning approach to de-noise optical coherence tomography (OCT) B-scans of the optic nerve head (ONH). Methods: Volume scans consisting of 97 horizontal B-scans were acquired through the center of the ONH using a commercial OCT device (Spectralis) for both eyes of 20 subjects. For each eye, single-frame (without signal averaging), and multi-frame (75x signal averaging) volume scans were obtained. A custom deep learning network was then designed and trained with 2,328 "clean B-scans" (multi-frame B-scans), and their corresponding "noisy B-scans" (clean B-scans + gaussian noise) to de-noise the single-frame B-scans. The performance of the de-noising algorithm was assessed qualitatively, and quantitatively on 1,552 B-scans using the signal to noise ratio (SNR), contrast to noise ratio (CNR), and mean structural similarity index metrics (MSSIM). Results: The proposed algorithm successfully denoised unseen single-frame OCT B-scans. The denoised B-scans were qualitatively similar to their corresponding multi-frame B-scans, with enhanced visibility of the ONH tissues. The mean SNR increased from $4.02 \pm 0.68$ dB (single-frame) to $8.14 \pm 1.03$ dB (denoised). For all the ONH tissues, the mean CNR increased from $3.50 \pm 0.56$ (single-frame) to $7.63 \pm 1.81$ (denoised). The MSSIM increased from $0.13 \pm 0.02$ (single frame) to $0.65 \pm 0.03$ (denoised) when compared with the corresponding multi-frame B-scans. Conclusions: Our deep learning algorithm can denoise a single-frame OCT B-scan of the ONH in under 20 ms, thus offering a framework to obtain superior quality OCT B-scans with reduced scanning times and minimal patient discomfort

Information selection and fusion in vision systems

Handling the enormous amounts of data produced by data-intensive imaging systems, such as multi-camera surveillance systems and microscopes, is technically challenging. While image and video compression help to manage the data volumes, they do not address the basic problem of information overflow. In this PhD we tackle the problem in a more drastic way. We select information of interest to a specific vision task, and discard the rest. We also combine data from different sources into a single output product, which presents the information of interest to end users in a suitable, summarized format. We treat two types of vision systems. The first type is conventional light microscopes. During this PhD, we have exploited for the first time the potential of the curvelet transform for image fusion for depth-of-field extension, allowing us to combine the advantages of multi-resolution image analysis for image fusion with increased directional sensitivity. As a result, the proposed technique clearly outperforms state-of-the-art methods, both on real microscopy data and on artificially generated images. The second type is camera networks with overlapping fields of view. To enable joint processing in such networks, inter-camera communication is essential. Because of infrastructure costs, power consumption for wireless transmission, etc., transmitting high-bandwidth video streams between cameras should be avoided. Fortunately, recently designed 'smart cameras', which have on-board processing and communication hardware, allow distributing the required image processing over the cameras. This permits compactly representing useful information from each camera. We focus on representing information for people localization and observation, which are important tools for statistical analysis of room usage, quick localization of people in case of building fires, etc. To further save bandwidth, we select which cameras should be involved in a vision task and transmit observations only from the selected cameras. We provide an information-theoretically founded framework for general purpose camera selection based on the Dempster-Shafer theory of evidence. Applied to tracking, it allows tracking people using a dynamic selection of as little as three cameras with the same accuracy as when using up to ten cameras

Terabyte-scale supervised 3D training and benchmarking dataset of the mouse kidney

The performance of machine learning algorithms, when used for segmenting 3D biomedical images, does not reach the level expected based on results achieved with 2D photos. This may be explained by the comparative lack of high-volume, high-quality training datasets, which require state-of-the-art imaging facilities, domain experts for annotation and large computational and personal resources. The HR-Kidney dataset presented in this work bridges this gap by providing 1.7 TB of artefact-corrected synchrotron radiation-based X-ray phase-contrast microtomography images of whole mouse kidneys and validated segmentations of 33 729 glomeruli, which corresponds to a one to two orders of magnitude increase over currently available biomedical datasets. The image sets also contain the underlying raw data, threshold- and morphology-based semi-automatic segmentations of renal vasculature and uriniferous tubules, as well as true 3D manual annotations. We therewith provide a broad basis for the scientific community to build upon and expand in the fields of image processing, data augmentation and machine learning, in particular unsupervised and semi-supervised learning investigations, as well as transfer learning and generative adversarial networks

Signal processing with Fourier analysis, novel algorithms and applications

Fourier analysis is the study of the way general functions may be represented or approximated by sums of simpler trigonometric functions, also analogously known as sinusoidal modeling. The original idea of Fourier had a profound impact on mathematical analysis, physics and engineering because it diagonalizes time-invariant convolution operators. In the past signal processing was a topic that stayed almost exclusively in electrical engineering, where only the experts could cancel noise, compress and reconstruct signals. Nowadays it is almost ubiquitous, as everyone now deals with modern digital signals. Medical imaging, wireless communications and power systems of the future will experience more data processing conditions and wider range of applications requirements than the systems of today. Such systems will require more powerful, efficient and flexible signal processing algorithms that are well designed to handle such needs. No matter how advanced our hardware technology becomes we will still need intelligent and efficient algorithms to address the growing demands in signal processing. In this thesis, we investigate novel techniques to solve a suite of four fundamental problems in signal processing that have a wide range of applications. The relevant equations, literature of signal processing applications, analysis and final numerical algorithms/methods to solve them using Fourier analysis are discussed for different applications in the electrical engineering/computer science. The first four chapters cover the following topics of central importance in the field of signal processing: • Fast Phasor Estimation using Adaptive Signal Processing (Chapter 2) • Frequency Estimation from Nonuniform Samples (Chapter 3) • 2D Polar and 3D Spherical Polar Nonuniform Discrete Fourier Transform (Chapter 4) • Robust 3D registration using Spherical Polar Discrete Fourier Transform and Spherical Harmonics (Chapter 5) Even though each of these four methods discussed may seem completely disparate, the underlying motivation for more efficient processing by exploiting the Fourier domain signal structure remains the same. The main contribution of this thesis is the innovation in the analysis, synthesis, discretization of certain well known problems like phasor estimation, frequency estimation, computations of a particular non-uniform Fourier transform and signal registration on the transformed domain. We conduct propositions and evaluations of certain applications relevant algorithms such as, frequency estimation algorithm using non-uniform sampling, polar and spherical polar Fourier transform. The techniques proposed are also useful in the field of computer vision and medical imaging. From a practical perspective, the proposed algorithms are shown to improve the existing solutions in the respective fields where they are applied/evaluated. The formulation and final proposition is shown to have a variety of benefits. Future work with potentials in medical imaging, directional wavelets, volume rendering, video/3D object classifications, high dimensional registration are also discussed in the final chapter. Finally, in the spirit of reproducible research we release the implementation of these algorithms to the public using Github

Terabyte-scale supervised 3D training and benchmarking dataset of the mouse kidney

The performance of machine learning algorithms, when used for segmenting 3D biomedical images, does not reach the level expected based on results achieved with 2D photos. This may be explained by the comparative lack of high-volume, high-quality training datasets, which require state-of-the-art imaging facilities, domain experts for annotation and large computational and personal resources. The HR-Kidney dataset presented in this work bridges this gap by providing 1.7 TB of artefact-corrected synchrotron radiation-based X-ray phase-contrast microtomography images of whole mouse kidneys and validated segmentations of 33 729 glomeruli, which corresponds to a one to two orders of magnitude increase over currently available biomedical datasets. The image sets also contain the underlying raw data, threshold- and morphology-based semi-automatic segmentations of renal vasculature and uriniferous tubules, as well as true 3D manual annotations. We therewith provide a broad basis for the scientific community to build upon and expand in the fields of image processing, data augmentation and machine learning, in particular unsupervised and semi-supervised learning investigations, as well as transfer learning and generative adversarial networks

3D FACE RECOGNITION USING LOCAL FEATURE BASED METHODS

Face recognition has attracted many researchers’ attention compared to other biometrics due to its non-intrusive and friendly nature. Although several methods for 2D face recognition have been proposed so far, there are still some challenges related to the 2D face including illumination, pose variation, and facial expression. In the last few decades, 3D face research area has become more interesting since shape and geometry information are used to handle challenges from 2D faces. Existing algorithms for face recognition are divided into three different categories: holistic feature-based, local feature-based, and hybrid methods. According to the literature, local features have shown better performance relative to holistic feature-based methods under expression and occlusion challenges. In this dissertation, local feature-based methods for 3D face recognition have been studied and surveyed. In the survey, local methods are classified into three broad categories which consist of keypoint-based, curve-based, and local surface-based methods. Inspired by keypoint-based methods which are effective to handle partial occlusion, structural context descriptor on pyramidal shape maps and texture image has been proposed in a multimodal scheme. Score-level fusion is used to combine keypoints’ matching score in both texture and shape modalities. The survey shows local surface-based methods are efficient to handle facial expression. Accordingly, a local derivative pattern is introduced to extract distinct features from depth map in this work. In addition, the local derivative pattern is applied on surface normals. Most 3D face recognition algorithms are focused to utilize the depth information to detect and extract features. Compared to depth maps, surface normals of each point can determine the facial surface orientation, which provides an efficient facial surface representation to extract distinct features for recognition task. An Extreme Learning Machine (ELM)-based auto-encoder is used to make the feature space more discriminative. Expression and occlusion robust analysis using the information from the normal maps are investigated by dividing the facial region into patches. A novel hybrid classifier is proposed to combine Sparse Representation Classifier (SRC) and ELM classifier in a weighted scheme. The proposed algorithms have been evaluated on four widely used 3D face databases; FRGC, Bosphorus, Bu-3DFE, and 3D-TEC. The experimental results illustrate the effectiveness of the proposed approaches. The main contribution of this work lies in identification and analysis of effective local features and a classification method for improving 3D face recognition performance