Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data

Image matching techniques are proven to be necessary in various fields of science and engineering, with many new methods and applications introduced over the years. In this PhD thesis, several computational image matching methods are introduced and investigated for improving the analysis of various biomedical image data. These improvements include the use of matching techniques for enhancing visualization of cross-sectional imaging modalities such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), denoising of retinal Optical Coherence Tomography (OCT), and high quality 3D reconstruction of surfaces from Scanning Electron Microscope (SEM) images. This work greatly improves the process of data interpretation of image data with far reaching consequences for basic sciences research. The thesis starts with a general notion of the problem of image matching followed by an overview of the topics covered in the thesis. This is followed by introduction and investigation of several applications of image matching/registration in biomdecial image processing: a) registration-based slice interpolation, b) fast mesh-based deformable image registration and c) use of simultaneous rigid registration and Robust Principal Component Analysis (RPCA) for speckle noise reduction of retinal OCT images. Moving towards a different notion of image matching/correspondence, the problem of view synthesis and 3D reconstruction, with a focus on 3D reconstruction of microscopic samples from 2D images captured by SEM, is considered next. Starting from sparse feature-based matching techniques, an extensive analysis is provided for using several well-known feature detector/descriptor techniques, namely ORB, BRIEF, SURF and SIFT, for the problem of multi-view 3D reconstruction. This chapter contains qualitative and quantitative comparisons in order to reveal the shortcomings of the sparse feature-based techniques. This is followed by introduction of a novel framework using sparse-dense matching/correspondence for high quality 3D reconstruction of SEM images. As will be shown, the proposed framework results in better reconstructions when compared with state-of-the-art sparse-feature based techniques. Even though the proposed framework produces satisfactory results, there is room for improvements. These improvements become more necessary when dealing with higher complexity microscopic samples imaged by SEM as well as in cases with large displacements between corresponding points in micrographs. Therefore, based on the proposed framework, a new approach is proposed for high quality 3D reconstruction of microscopic samples. While in case of having simpler microscopic samples the performance of the two proposed techniques are comparable, the new technique results in more truthful reconstruction of highly complex samples. The thesis is concluded with an overview of the thesis and also pointers regarding future directions of the research using both multi-view and photometric techniques for 3D reconstruction of SEM images

Multiscale bilateral filtering for improving image quality in digital breast tomosynthesis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135115/1/mp3283.pd

Lattice-Based High-Dimensional Gaussian Filtering and the Permutohedral Lattice

High-dimensional Gaussian filtering is a popular technique in image processing, geometry processing and computer graphics for smoothing data while preserving important features. For instance, the bilateral filter, cross bilateral filter and non-local means filter fall under the broad umbrella of high-dimensional Gaussian filters. Recent algorithmic advances therein have demonstrated that by relying on a sampled representation of the underlying space, one can obtain speed-ups of orders of magnitude over the naïve approach. The simplest such sampled representation is a lattice, and it has been used successfully in the bilateral grid and the permutohedral lattice algorithms. In this paper, we analyze these lattice-based algorithms, developing a general theory of lattice-based high-dimensional Gaussian filtering. We consider the set of criteria for an optimal lattice for filtering, as it offers a good tradeoff of quality for computational efficiency, and evaluate the existing lattices under the criteria. In particular, we give a rigorous exposition of the properties of the permutohedral lattice and argue that it is the optimal lattice for Gaussian filtering. Lastly, we explore further uses of the permutohedral-lattice-based Gaussian filtering framework, showing that it can be easily adapted to perform mean shift filtering and yield improvement over the traditional approach based on a Cartesian grid.Stanford University (Reed-Hodgson Fellowship)Nokia Research Cente

Casual 3D photography

We present an algorithm that enables casual 3D photography. Given a set of input photos captured with a hand-held cell phone or DSLR camera, our algorithm reconstructs a 3D photo, a central panoramic, textured, normal mapped, multi-layered geometric mesh representation. 3D photos can be stored compactly and are optimized for being rendered from viewpoints that are near the capture viewpoints. They can be rendered using a standard rasterization pipeline to produce perspective views with motion parallax. When viewed in VR, 3D photos provide geometrically consistent views for both eyes. Our geometric representation also allows interacting with the scene using 3D geometry-aware effects, such as adding new objects to the scene and artistic lighting effects. Our 3D photo reconstruction algorithm starts with a standard structure from motion and multi-view stereo reconstruction of the scene. The dense stereo reconstruction is made robust to the imperfect capture conditions using a novel near envelope cost volume prior that discards erroneous near depth hypotheses. We propose a novel parallax-tolerant stitching algorithm that warps the depth maps into the central panorama and stitches two color-and-depth panoramas for the front and back scene surfaces. The two panoramas are fused into a single non-redundant, well-connected geometric mesh. We provide videos demonstrating users interactively viewing and manipulating our 3D photos

Learning Inference Models for Computer Vision

Computer vision can be understood as the ability to perform 'inference' on image data. Breakthroughs in computer vision technology are often marked by advances in inference techniques, as even the model design is often dictated by the complexity of inference in them. This thesis proposes learning based inference schemes and demonstrates applications in computer vision. We propose techniques for inference in both generative and discriminative computer vision models. Despite their intuitive appeal, the use of generative models in vision is hampered by the difficulty of posterior inference, which is often too complex or too slow to be practical. We propose techniques for improving inference in two widely used techniques: Markov Chain Monte Carlo (MCMC) sampling and message-passing inference. Our inference strategy is to learn separate discriminative models that assist Bayesian inference in a generative model. Experiments on a range of generative vision models show that the proposed techniques accelerate the inference process and/or converge to better solutions. A main complication in the design of discriminative models is the inclusion of prior knowledge in a principled way. For better inference in discriminative models, we propose techniques that modify the original model itself, as inference is simple evaluation of the model. We concentrate on convolutional neural network (CNN) models and propose a generalization of standard spatial convolutions, which are the basic building blocks of CNN architectures, to bilateral convolutions. First, we generalize the existing use of bilateral filters and then propose new neural network architectures with learnable bilateral filters, which we call `Bilateral Neural Networks'. We show how the bilateral filtering modules can be used for modifying existing CNN architectures for better image segmentation and propose a neural network approach for temporal information propagation in videos. Experiments demonstrate the potential of the proposed bilateral networks on a wide range of vision tasks and datasets. In summary, we propose learning based techniques for better inference in several computer vision models ranging from inverse graphics to freely parameterized neural networks. In generative vision models, our inference techniques alleviate some of the crucial hurdles in Bayesian posterior inference, paving new ways for the use of model based machine learning in vision. In discriminative CNN models, the proposed filter generalizations aid in the design of new neural network architectures that can handle sparse high-dimensional data as well as provide a way for incorporating prior knowledge into CNNs