Locally Adaptive Stereo Vision Based 3D Visual Reconstruction

abstract: Using stereo vision for 3D reconstruction and depth estimation has become a popular and promising research area as it has a simple setup with passive cameras and relatively efficient processing procedure. The work in this dissertation focuses on locally adaptive stereo vision methods and applications to different imaging setups and image scenes. Solder ball height and substrate coplanarity inspection is essential to the detection of potential connectivity issues in semi-conductor units. Current ball height and substrate coplanarity inspection tools are expensive and slow, which makes them difficult to use in a real-time manufacturing setting. In this dissertation, an automatic, stereo vision based, in-line ball height and coplanarity inspection method is presented. The proposed method includes an imaging setup together with a computer vision algorithm for reliable, in-line ball height measurement. The imaging setup and calibration, ball height estimation and substrate coplanarity calculation are presented with novel stereo vision methods. The results of the proposed method are evaluated in a measurement capability analysis (MCA) procedure and compared with the ground-truth obtained by an existing laser scanning tool and an existing confocal inspection tool. The proposed system outperforms existing inspection tools in terms of accuracy and stability. In a rectified stereo vision system, stereo matching methods can be categorized into global methods and local methods. Local stereo methods are more suitable for real-time processing purposes with competitive accuracy as compared with global methods. This work proposes a stereo matching method based on sparse locally adaptive cost aggregation. In order to reduce outlier disparity values that correspond to mis-matches, a novel sparse disparity subset selection method is proposed by assigning a significance status to candidate disparity values, and selecting the significant disparity values adaptively. An adaptive guided filtering method using the disparity subset for refined cost aggregation and disparity calculation is demonstrated. The proposed stereo matching algorithm is tested on the Middlebury and the KITTI stereo evaluation benchmark images. A performance analysis of the proposed method in terms of the I0 norm of the disparity subset is presented to demonstrate the achieved efficiency and accuracy.Dissertation/ThesisDoctoral Dissertation Electrical Engineering 201

Multimodal Biomedical Data Visualization: Enhancing Network, Clinical, and Image Data Depiction

In this dissertation, we present visual analytics tools for several biomedical applications. Our research spans three types of biomedical data: reaction networks, longitudinal multidimensional clinical data, and biomedical images. For each data type, we present intuitive visual representations and efficient data exploration methods to facilitate visual knowledge discovery. Rule-based simulation has been used for studying complex protein interactions. In a rule-based model, the relationships of interacting proteins can be represented as a network. Nevertheless, understanding and validating the intended behaviors in large network models are ineffective and error prone. We have developed a tool that first shows a network overview with concise visual representations and then shows relevant rule-specific details on demand. This strategy significantly improves visualization comprehensibility and disentangles the complex protein-protein relationships by showing them selectively alongside the global context of the network. Next, we present a tool for analyzing longitudinal multidimensional clinical datasets, that we developed for understanding Parkinson's disease progression. Detecting patterns involving multiple time-varying variables is especially challenging for clinical data. Conventional computational techniques, such as cluster analysis and dimension reduction, do not always generate interpretable, actionable results. Using our tool, users can select and compare patient subgroups by filtering patients with multiple symptoms simultaneously and interactively. Unlike conventional visualizations that use local features, many targets in biomedical images are characterized by high-level features. We present our research characterizing such high-level features through multiscale texture segmentation and deep-learning strategies. First, we present an efficient hierarchical texture segmentation approach that scales up well to gigapixel images to colorize electron microscopy (EM) images. This enhances visual comprehensibility of gigapixel EM images across a wide range of scales. Second, we use convolutional neural networks (CNNs) to automatically derive high-level features that distinguish cell states in live-cell imagery and voxel types in 3D EM volumes. In addition, we present a CNN-based 3D segmentation method for biomedical volume datasets with limited training samples. We use factorized convolutions and feature-level augmentations to improve model generalization and avoid overfitting

A machine learning approach to the unsupervised segmentation of mitochondria in subcellular electron microscopy data

Recent advances in cellular and subcellular microscopy demonstrated its potential towards unravelling the mechanisms of various diseases at the molecular level. The biggest challenge in both human- and computer-based visual analysis of micrographs is the variety of nanostructures and mitochondrial morphologies. The state-of-the-art is, however, dominated by supervised manual data annotation and early attempts to automate the segmentation process were based on supervised machine learning techniques which require large datasets for training. Given a minimal number of training sequences or none at all, unsupervised machine learning formulations, such as spectral dimensionality reduction, are known to be superior in detecting salient image structures. This thesis presents three major contributions developed around the spectral clustering framework which is proven to capture perceptual organization features. Firstly, we approach the problem of mitochondria localization. We propose a novel grouping method for the extracted line segments which describes the normal mitochondrial morphology. Experimental findings show that the clusters obtained successfully model the inner mitochondrial membrane folding and therefore can be used as markers for the subsequent segmentation approaches. Secondly, we developed an unsupervised mitochondria segmentation framework. This method follows the evolutional ability of human vision to extrapolate salient membrane structures in a micrograph. Furthermore, we designed robust non-parametric similarity models according to Gestaltic laws of visual segregation. Experiments demonstrate that such models automatically adapt to the statistical structure of the biological domain and return optimal performance in pixel classification tasks under the wide variety of distributional assumptions. The last major contribution addresses the computational complexity of spectral clustering. Here, we introduced a new anticorrelation-based spectral clustering formulation with the objective to improve both: speed and quality of segmentation. The experimental findings showed the applicability of our dimensionality reduction algorithm to very large scale problems as well as asymmetric, dense and non-Euclidean datasets

The HBP1 tumor suppressor is a negative epigenetic regulator of MYCN driven neuroblastoma through interaction with the PRC2 complex

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