Visual Quality Enhancement in Optoacoustic Tomography using Active Contour Segmentation Priors

Segmentation of biomedical images is essential for studying and characterizing anatomical structures, detection and evaluation of pathological tissues. Segmentation has been further shown to enhance the reconstruction performance in many tomographic imaging modalities by accounting for heterogeneities of the excitation field and tissue properties in the imaged region. This is particularly relevant in optoacoustic tomography, where discontinuities in the optical and acoustic tissue properties, if not properly accounted for, may result in deterioration of the imaging performance. Efficient segmentation of optoacoustic images is often hampered by the relatively low intrinsic contrast of large anatomical structures, which is further impaired by the limited angular coverage of some commonly employed tomographic imaging configurations. Herein, we analyze the performance of active contour models for boundary segmentation in cross-sectional optoacoustic tomography. The segmented mask is employed to construct a two compartment model for the acoustic and optical parameters of the imaged tissues, which is subsequently used to improve accuracy of the image reconstruction routines. The performance of the suggested segmentation and modeling approach are showcased in tissue-mimicking phantoms and small animal imaging experiments.Comment: Accepted for publication in IEEE Transactions on Medical Imagin

Joint Reconstruction of Multi-channel, Spectral CT Data via Constrained Total Nuclear Variation Minimization

We explore the use of the recently proposed "total nuclear variation" (TNV) as a regularizer for reconstructing multi-channel, spectral CT images. This convex penalty is a natural extension of the total variation (TV) to vector-valued images and has the advantage of encouraging common edge locations and a shared gradient direction among image channels. We show how it can be incorporated into a general, data-constrained reconstruction framework and derive update equations based on the first-order, primal-dual algorithm of Chambolle and Pock. Early simulation studies based on the numerical XCAT phantom indicate that the inter-channel coupling introduced by the TNV leads to better preservation of image features at high levels of regularization, compared to independent, channel-by-channel TV reconstructions.Comment: Submitted to Physics in Medicine and Biolog

Science Requirements and Conceptual Design for a Polarized Medium Energy Electron-Ion Collider at Jefferson Lab

This report presents a brief summary of the science opportunities and program of a polarized medium energy electron-ion collider at Jefferson Lab and a comprehensive description of the conceptual design of such a collider based on the CEBAF electron accelerator facility.Comment: 160 pages, ~93 figures This work was supported by the U.S. Department of Energy, Office of Nuclear Physics, under Contract No. DE-AC05-06OR23177, DE-AC02-06CH11357, DE-AC05-060R23177, and DESC0005823. The U.S. Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce this manuscript for U.S. Government purpose

Components of bottom-up gaze allocation in natural images

Recent research [Parkhurst, D., Law, K., & Niebur, E., 2002. Modeling the role of salience in the allocation of overt visual attention. Vision Research 42 (1) (2002) 107–123] showed that a model of bottom-up visual attention can account in part for the spatial locations fixated by humans while free-viewing complex natural and artificial scenes. That study used a definition of salience based on local detectors with coarse global surround inhibition. Here, we use a similar framework to investigate the roles of several types of non-linear interactions known to exist in visual cortex, and of eccentricity-dependent processing. For each of these, we added a component to the salience model, including richer interactions among orientation-tuned units, both at spatial short range (for clutter reduction) and long range (for contour facilitation), and a detailed model of eccentricity-dependent changes in visual processing. Subjects free-viewed naturalistic and artificial images while their eye movements were recorded, and the resulting fixation locations were compared with the models’ predicted salience maps. We found that the proposed interactions indeed play a significant role in the spatiotemporal deployment of attention in natural scenes; about half of the observed inter-subject variance can be explained by these different models. This suggests that attentional guidance does not depend solely on local visual features, but must also include the effects of interactions among features. As models of these interactions become more accurate in predicting behaviorally-relevant salient locations, they become useful to a range of applications in computer vision and human-machine interface design

On Motion Parameterizations in Image Sequences from Fixed Viewpoints

This dissertation addresses the problem of parameterizing object motion within a set of images taken with a stationary camera. We develop data-driven methods across all image scales: characterizing motion observed at the scale of individual pixels, along extended structures such as roads, and whole image deformations such as lungs deforming over time. The primary contributions include: a) fundamental studies of the relationship between spatio-temporal image derivatives accumulated at a pixel, and the object motions at that pixel,: b) data driven approaches to parameterize breath motion and reconstruct lung CT data volumes, and: c) defining and offering initial results for a new class of Partially Unsupervised Manifold Learning: PUML) problems, which often arise in medical imagery. Specifically, we create energy functions for measuring how consistent a given velocity vector is with observed spatio-temporal image derivatives. These energy functions are used to fit parametric snake models to roads using velocity constraints. We create an automatic data-driven technique for finding the breath phase of lung CT scans which is able to replace external belt measurements currently in use clinically. This approach is extended to automatically create a full deformation model of a CT lung volume during breathing or heart MRI during breathing and heartbeat. Additionally, motivated by real use cases, we address a scenario in which a dataset is collected along with meta-data which describes some, but not all, aspects of the dataset. We create an embedding which displays the remaining variability in a dataset after accounting for variability related to the meta-data

Automated Visual Database Creation For A Ground Vehicle Simulator

This research focuses on extracting road models from stereo video sequences taken from a moving vehicle. The proposed method combines color histogram based segmentation, active contours (snakes) and morphological processing to extract road boundary coordinates for conversion into Matlab or Multigen OpenFlight compatible polygonal representations. Color segmentation uses an initial truth frame to develop a color probability density function (PDF) of the road versus the terrain. Subsequent frames are segmented using a Maximum Apostiori Probability (MAP) criteria and the resulting templates are used to update the PDFs. Color segmentation worked well where there was minimal shadowing and occlusion by other cars. A snake algorithm was used to find the road edges which were converted to 3D coordinates using stereo disparity and vehicle position information. The resulting 3D road models were accurate to within 1 meter

Novel image markers for non-small cell lung cancer classification and survival prediction

BACKGROUND: Non-small cell lung cancer (NSCLC), the most common type of lung cancer, is one of serious diseases causing death for both men and women. Computer-aided diagnosis and survival prediction of NSCLC, is of great importance in providing assistance to diagnosis and personalize therapy planning for lung cancer patients. RESULTS: In this paper we have proposed an integrated framework for NSCLC computer-aided diagnosis and survival analysis using novel image markers. The entire biomedical imaging informatics framework consists of cell detection, segmentation, classification, discovery of image markers, and survival analysis. A robust seed detection-guided cell segmentation algorithm is proposed to accurately segment each individual cell in digital images. Based on cell segmentation results, a set of extensive cellular morphological features are extracted using efficient feature descriptors. Next, eight different classification techniques that can handle high-dimensional data have been evaluated and then compared for computer-aided diagnosis. The results show that the random forest and adaboost offer the best classification performance for NSCLC. Finally, a Cox proportional hazards model is fitted by component-wise likelihood based boosting. Significant image markers have been discovered using the bootstrap analysis and the survival prediction performance of the model is also evaluated. CONCLUSIONS: The proposed model have been applied to a lung cancer dataset that contains 122 cases with complete clinical information. The classification performance exhibits high correlations between the discovered image markers and the subtypes of NSCLC. The survival analysis demonstrates strong prediction power of the statistical model built from the discovered image markers

Fundamentals and applications of spatial dissipative solitons in photonic devices : [Chapter 6]

We review the properties of optical spatial dissipative solitons (SDS). These are stable, self‐localized optical excitations sitting on a uniform, or quasi‐uniform, background in a dissipative environment like a nonlinear optical cavity. Indeed, in optics they are often termed “cavity solitons.” We discuss their dynamics and interactions in both ideal and imperfect systems, making comparison with experiments. SDS in lasers offer important advantages for applications. We review candidate schemes and the tremendous recent progress in semiconductor‐based cavity soliton lasers. We examine SDS in periodic structures, and we show how SDS can be quantitatively related to the locking of fronts. We conclude with an assessment of potential applications of SDS in photonics, arguing that best use of their particular features is made by exploiting their mobility, for example in all‐optical delay lines

Perception-Action Coupling Target Tracking Control for a Snake Robot via Reinforcement Learning

Visual-guided locomotion for snake-like robots is a challenging task, since it involves not only the complex body undulation with many joints, but also a joint pipeline that connects the vision and the locomotion. Meanwhile, it is usually difficult to jointly coordinate these two separate sub-tasks as this requires time-consuming and trial-and-error tuning. In this paper, we introduce a novel approach for solving target tracking tasks for a snake-like robot as a whole using a model-free reinforcement learning (RL) algorithm. This RL-based controller directly maps the visual observations to the joint positions of the snake-like robot in an end-to-end fashion instead of dividing the process into a series of sub-tasks. With a novel customized reward function, our RL controller is trained in a dynamically changing track scenario. The controller is evaluated in four different tracking scenarios and the results show excellent adaptive locomotion ability to the unpredictable behavior of the target. Meanwhile, the results also prove that the RL-based controller outperforms the traditional model-based controller in terms of tracking accuracy

Novel Image Markers for Non-Small Cell Lung Cancer Classification and Survival Prediction

BACKGROUND: Non-small cell lung cancer (NSCLC), the most common type of lung cancer, is one of serious diseases causing death for both men and women. Computer-aided diagnosis and survival prediction of NSCLC, is of great importance in providing assistance to diagnosis and personalize therapy planning for lung cancer patients. RESULTS: In this paper we have proposed an integrated framework for NSCLC computer-aided diagnosis and survival analysis using novel image markers. The entire biomedical imaging informatics framework consists of cell detection, segmentation, classification, discovery of image markers, and survival analysis. A robust seed detection-guided cell segmentation algorithm is proposed to accurately segment each individual cell in digital images. Based on cell segmentation results, a set of extensive cellular morphological features are extracted using efficient feature descriptors. Next, eight different classification techniques that can handle high-dimensional data have been evaluated and then compared for computer-aided diagnosis. The results show that the random forest and adaboost offer the best classification performance for NSCLC. Finally, a Cox proportional hazards model is fitted by component-wise likelihood based boosting. Significant image markers have been discovered using the bootstrap analysis and the survival prediction performance of the model is also evaluated. CONCLUSIONS: The proposed model have been applied to a lung cancer dataset that contains 122 cases with complete clinical information. The classification performance exhibits high correlations between the discovered image markers and the subtypes of NSCLC. The survival analysis demonstrates strong prediction power of the statistical model built from the discovered image markers