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We consider the restoration of blurred images corrupted by Poisson noise using variance-stabilizing transformations (VST). Although VST are an established tool used extensively for denoising, their adoption in deconvolution problems is problematic because VST are necessarily nonlinear operators, and thus break the linear image-formation model typically adopted in deconvolution. We propose a deblurring...
Exploring the spatial interactions between tumor and the inflammatory microenvironment using digital pathology image analysis can contribute to a better understanding of the immune function and tumor heterogeneity. We address this by providing tools able to reveal various metrics describing spatial relationships in the cancer ecosystem. The approach comprises nuclei segmentation and classification,...
Automatic MR whole prostate segmentation is a challenging task. Recent approaches have attempted to harness the capabilities of deep learning for MR prostate segmentation to tackle pixel-level labeling tasks. Patch-based and hierarchical features-based deep CNN models were used to delineate the prostate boundary. To further investigate this problem, we introduce a Holistically-Nested Edge Detector...
Axon diameter estimation has been a focus of the diffusion MRI community for the past decade. The main argument has been that while diffusion models always overestimate the true axon diameter, their estimation still correlates with changes in true value. Until now, this remains more as a discussion point. The aim of this paper is to clarify this hypothesis using a recently acquired cat spinal cord...
White matter segmentation is an essential step to study whole-brain structural connectivity via diffusion MRI white matter tractography. One important goal of segmentation methods is to improve consistency of the white matter segmentations across multiple subjects. In this study, we quantitatively compare two popular white matter segmentation strategies, i.e., a cortical-parcellation-based method...
Biological membranes are one of the most basic structures and regions of interest in cell biology. In the study of membranes, segment extraction is a well-known and difficult problem because of impeding noise, directional and thickness variability, etc. Recent advances in electron microscopy membrane segmentation are able to cope with such difficulties by training convolutional neural networks. However,...
Early and more sensitive detection of small aneurysms in 3D cerebral angiograms is required to prevent potentially fatal rupture events. Herein, we propose a novel method that entails structure enhancement filtering to highlight potential aneurysm locations, intra-vascular distance mapping for regional vascular shape encoding and dimensionality reduction and a convolutional neural network to automatically...
Patients with major depressive disorder (MDD) who do not achieve full symptomatic recovery after antidepressant treatment have a higher risk of relapse. Compared to pharmacotherapies, electroconvulsive therapy (ECT) more rapidly produces a greater extent of response in severely depressed patients. However, prediction of which candidates are most likely to improve after ECT remains challenging. Using...
Resting-state fMRI provides challenging data that needs to be analyzed without knowledge about timing or duration of neuronal events. The “total activation” framework is one recent approach that combines temporal and spatial regularization to deconvolve the fMRI signals; i.e., undo them from the influence of the hemodynamic response. The temporal regularization is using generalized total variation...
Recently, C-arm cone-beam CT systems have been used to acquire knee joints under weight-bearing conditions. For this purpose, the C-arm acquires images on a horizontal trajectory around the standing patient, who shows involuntary motion. The current state-of-the-art reconstruction approach estimates motion based on fiducial markers attached to the knee. A drawback is that this method requires calibration...
This paper addresses a dense voxel-wise correspondence of cone-beam computed tomography (CBCT) images towards a non-rigid registration and treatments evaluation in clinical orthodontics. An unsupervised clustering randomized forest is employed to establish voxel-wise correspondence in a reduced subset of the original volume image. A geodesic coordinate is introduced to avoid the structural ambiguities...
Chest tomosynthesis (CTS) is a newly developed imaging technique which provides pseudo-3D volume anatomical information of thorax from limited angle projections and therefore improves the visibility of anatomy without so much increase on radiation dose compared to the chest radiography (CXR). However, one of the relatively common problems in CTS is the respiratory motion of patient during image acquisition,...
Multisubject analysis helps to jointly analyze themedical data from multiple subjects, to make insightful inferences. Multi set canonical correlation analysis (MCCA), which extends the application of canonical correlation analysis to more than two datasets, is one such statistical technique to perform multisubject analysis. MCCA aims to compute optimal data transformations such that overall correlation...
Accurate registration plays a critical role in group-wise functional Magnetic Resonance Imaging (fMRI) image analysis, as spatial correspondence among different brain images is a prerequisite for inferring meaningful patterns. However, the problem is challenging and remains open, and more effort should be made to advance the state-of-the-art image registration methods for fMRI images. Inspired by...
This paper addresses the estimation of pairwise supervoxel correspondences toward automatic semi-dense medical image registration. Supervoxel matching is performed through random forests (RF) with supervoxel indexes as label entities to predict matching areas in another target image. Ensuring accurate supervoxel boundary adherence requires a fine supervoxel decomposition which highly increases learning...
Non-local means (NLM) filtering of fMRI can reduce noise while preserving spatial structure. We have developed a variant called temporal-NLM (tNLM) which uses similarity in time-series between voxels as the basis for computing the weights in the filter. Using tNLM, dynamic fMRI data can be denoised while spatial boundaries between functionally distinct areas in the brain tend to be preserved. The...
Segmentation of skin lesions is considered as an important step in computer aided diagnosis (CAD) for melanoma diagnosis. There have many attempts to segment skin lesions in a semi- or fully-automated manner. Existing methods, however, have problems with over- or under-segmentation and do not perform well with challenging skin lesions such as when a lesion is partially connected to the background...
Detection and segmentation of small renal mass (SRM) in renal CT images are important pre-processing for computer-aided diagnosis of renal cancer. However, the task is known to be challenging due to its variety of size, shape, and location. In this paper, we propose an automated method for detecting and segmenting SRM in contrast-enhanced CT images using texture and context feature classification...
Iterative image reconstruction algorithms have the potential to reduce the radiation dose in computed tomography (CT), but they are computationally intensive and their performance usually depends on careful parameter tuning. In this paper, we propose an iterative CT reconstruction algorithm based on the new class of variance-reduced stochastic gradient descent (VR-SGD) algorithms. Our experiments...
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