Retinal layer thickness, evaluated as a function of spatial position from optical coherence tomography (OCT) images is an important diagnostics marker for many retinal diseases. However, due to factors such as speckle noise, low image contrast, irregularly shaped morphological features such as retinal detachments, macular holes, and drusen, accurate segmentation of individual retinal layers is difficult. To address this issue, a computer method for retinal layer segmentation from OCT images is presented. An efficient two-step kernel-based optimization scheme is employed to first identify the approximate locations of the individual layers, which are then refined to obtain accurate segmentation results for the individual layers. The performance of the algorithm was tested on a set of retinal images acquired in-vivo from healthy and diseased rodent models with a high speed, high resolution OCT system. Experimental results show that the proposed approach provides accurate segmentation for OCT images affected by speckle noise, even in sub-optimal conditions of low image contrast and presence of irregularly shaped structural features in the OCT images.

An important image post-processing step for optical coherence tomography (OCT) images is speckle noise reduction. Noise in OCT images is multiplicative in nature and is difficult to suppress due to the fact that in addition the noise component, OCT speckle also carries structural information about the imaged object. To address this issue, a novel speckle noise reduction algorithm was developed. The algorithm projects the imaging data into the logarithmic space and a general Bayesian least squares estimate of the noise-free data is found using a conditional posterior sampling approach. The proposed algorithm was tested on a number of rodent (rat) retina images acquired in-vivo with an ultrahigh resolution OCT system. The performance of the algorithm was compared to that of the state-of-the-art algorithms currently available for speckle denoising, such as the adaptive median, maximum a posteriori (MAP) estimation, linear least squares estimation, anisotropic diffusion and wavelet-domain filtering methods. Experimental results show that the proposed approach is capable of achieving state-of-the-art performance when compared to the other tested methods in terms of signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), edge preservation, and equivalent number of looks (ENL) measures. Visual comparisons also show that the proposed approach provides effective speckle noise suppression while preserving the sharpness and improving the visibility of morphological details, such as tiny capillaries and thin layers in the rat retina OCT images.

In this paper, we address the hyperspectral image (HSI) classification task with a generative adversarial network and conditional random field (GAN-CRF)-based framework, which integrates a semisupervised deep learning and a probabilistic graphical model, and make three contributions. First, we design four types of convolutional and transposed convolutional layers that consider the characteristics of HSIs to help with extracting discriminative features from limited numbers of labeled HSI samples. Second, we construct semisupervised generative adversarial networks (GANs) to alleviate the shortage of training samples by adding labels to them and implicitly reconstructing real HSI data distribution through adversarial training. Third, we build dense conditional random fields (CRFs) on top of the random variables that are initialized to the softmax predictions of the trained GANs and are conditioned on HSIs to refine classification maps. This semisupervised framework leverages the merits of discriminative and generative models through a game-theoretical approach. Moreover, even though we used very small numbers of labeled training HSI samples from the two most challenging and extensively studied datasets, the experimental results demonstrated that spectral-spatial GAN-CRF (SS-GAN-CRF) models achieved top-ranking accuracy for semisupervised HSI classification.

Prostate cancer is the most common form of cancer and the second leading cause of cancer death in North America. Auto-detection of prostate cancer can play a major role in early detection of prostate cancer, which has a significant impact on patient survival rates. While multi-parametric magnetic resonance imaging (MP-MRI) has shown promise in diagnosis of prostate cancer, the existing auto-detection algorithms do not take advantage of abundance of data available in MP-MRI to improve detection accuracy. The goal of this research was to design a radiomics-based auto-detection method for prostate cancer via utilizing MP-MRI data. In this work, we present new MP-MRI texture feature models for radiomics-driven detection of prostate cancer. In addition to commonly used non-invasive imaging sequences in conventional MP-MRI, namely T2-weighted MRI (T2w) and diffusion-weighted imaging (DWI), our proposed MP-MRI texture feature models incorporate computed high-b DWI (CHB-DWI) and a new diffusion imaging modality called correlated diffusion imaging (CDI). Moreover, the proposed texture feature models incorporate features from individual b-value images. A comprehensive set of texture features was calculated for both the conventional MP-MRI and new MP-MRI texture feature models. We performed feature selection analysis for each individual modality and then combined best features from each modality to construct the optimized texture feature models. The performance of the proposed MP-MRI texture feature models was evaluated via leave-one-patient-out cross-validation using a support vector machine (SVM) classifier trained on 40,975 cancerous and healthy tissue samples obtained from real clinical MP-MRI datasets. The proposed MP-MRI texture feature models outperformed the conventional model (i.e., T2w+DWI) with regard to cancer detection accuracy. Comprehensive texture feature models were developed for improved radiomics-driven detection of prostate cancer using MP-MRI. Using a comprehensive set of texture features and a feature selection method, optimal texture feature models were constructed that improved the prostate cancer auto-detection significantly compared to conventional MP-MRI texture feature models.

An automatic method for segmenting skin lesions in conventional macroscopic images is presented. The images are acquired with conventional cameras, without the use of a dermoscope. Automatic segmentation of skin lesions from macroscopic images is a very challenging problem due to factors such as illumination variations, irregular structural and color variations, the presence of hair, as well as the occurrence of multiple unhealthy skin regions. To address these factors, a novel iterative stochastic region-merging approach is employed to segment the regions corresponding to skin lesions from the macroscopic images, where stochastic region merging is initialized first on a pixel level, and subsequently on a region level until convergence. A region merging likelihood function based on the regional statistics is introduced to determine the merger of regions in a stochastic manner. Experimental results show that the proposed system achieves overall segmentation error of under 10% for skin lesions in macroscopic images, which is lower than that achieved by existing methods.