Pattern identification of biomedical images with time series: contrasting THz pulse imaging with DCE-MRIs

Objective We provide a survey of recent advances in biomedical image analysis and classification from emergent imaging modalities such as terahertz (THz) pulse imaging (TPI) and dynamic contrast-enhanced magnetic resonance images (DCE-MRIs) and identification of their underlining commonalities. Methods Both time and frequency domain signal pre-processing techniques are considered: noise removal, spectral analysis, principal component analysis (PCA) and wavelet transforms. Feature extraction and classification methods based on feature vectors using the above processing techniques are reviewed. A tensorial signal processing de-noising framework suitable for spatiotemporal association between features in MRI is also discussed. Validation Examples where the proposed methodologies have been successful in classifying TPIs and DCE-MRIs are discussed. Results Identifying commonalities in the structure of such heterogeneous datasets potentially leads to a unified multi-channel signal processing framework for biomedical image analysis. Conclusion The proposed complex valued classification methodology enables fusion of entire datasets from a sequence of spatial images taken at different time stamps; this is of interest from the viewpoint of inferring disease proliferation. The approach is also of interest for other emergent multi-channel biomedical imaging modalities and of relevance across the biomedical signal processing community

A machine learning route between band mapping and band structure

The electronic band structure (BS) of solid state materials imprints the multidimensional and multi-valued functional relations between energy and momenta of periodically confined electrons. Photoemission spectroscopy is a powerful tool for its comprehensive characterization. A common task in photoemission band mapping is to recover the underlying quasiparticle dispersion, which we call band structure reconstruction. Traditional methods often focus on specific regions of interests yet require extensive human oversight. To cope with the growing size and scale of photoemission data, we develop a generic machine-learning approach leveraging the information within electronic structure calculations for this task. We demonstrate its capability by reconstructing all fourteen valence bands of tungsten diselenide and validate the accuracy on various synthetic data. The reconstruction uncovers previously inaccessible momentum-space structural information on both global and local scales in conjunction with theory, while realizing a path towards integrating band mapping data into materials science databases

Light field image processing: an overview

Light field imaging has emerged as a technology allowing to capture richer visual information from our world. As opposed to traditional photography, which captures a 2D projection of the light in the scene integrating the angular domain, light fields collect radiance from rays in all directions, demultiplexing the angular information lost in conventional photography. On the one hand, this higher dimensional representation of visual data offers powerful capabilities for scene understanding, and substantially improves the performance of traditional computer vision problems such as depth sensing, post-capture refocusing, segmentation, video stabilization, material classification, etc. On the other hand, the high-dimensionality of light fields also brings up new challenges in terms of data capture, data compression, content editing, and display. Taking these two elements together, research in light field image processing has become increasingly popular in the computer vision, computer graphics, and signal processing communities. In this paper, we present a comprehensive overview and discussion of research in this field over the past 20 years. We focus on all aspects of light field image processing, including basic light field representation and theory, acquisition, super-resolution, depth estimation, compression, editing, processing algorithms for light field display, and computer vision applications of light field data

Large Growth Deformations of Thin Tissue using Solid-Shells

Simulating large scale expansion of thin structures, such as in growing leaves, is challenging. Sold-shells have a number of potential advantages over conventional thin-shell methods, but have thus far only been investigated for small plastic deformation cases. In response, we present a new general-purpose FEM growth framework for simulating large plastic deformations using a new solid-shell growth approach while supporting morphogen diffusion and collision handling. Large plastic deformations are handled by augmenting solid-shell elements with \textit{plastic embedding} and strain-aware adaptive remeshing. Plastic embedding is an approach to model large plastic deformations by modifying the rest configuration in response to displacement strain. We exploit the solid-shell's ability of describing both stretching and bending in terms of displacement strain to implement both plastic stretching and bending using the same plasticity model. The large deformations are adaptively remeshed using a strain-aware criteria to anticipate buckling and eliminate low-quality elements. We perform qualitative investigations on the capabilities of the new solid-shell growth approach in reproducing buckling, rippling, rolling, and collision deformations, relevant towards animating growing leaves, flowers, and other thin structures. The qualitative experiments demonstrates that solid-shells are a viable alternative to thin-shells for simulating large and intricate growth deformations

Visualization of Tensor Fields in Mechanics

Tensors are used to describe complex physical processes in many applications. Examples include the distribution of stresses in technical materials, acting forces during seismic events, or remodeling of biological tissues. While tensors encode such complex information mathematically precisely, the semantic interpretation of a tensor is challenging. Visualization can be beneficial here and is frequently used by domain experts. Typical strategies include the use of glyphs, color plots, lines, and isosurfaces. However, data complexity is nowadays accompanied by the sheer amount of data produced by large-scale simulations and adds another level of obstruction between user and data. Given the limitations of traditional methods, and the extra cognitive effort of simple methods, more advanced tensor field visualization approaches have been the focus of this work. This survey aims to provide an overview of recent research results with a strong application-oriented focus, targeting applications based on continuum mechanics, namely the fields of structural, bio-, and geomechanics. As such, the survey is complementing and extending previously published surveys. Its utility is twofold: (i) It serves as basis for the visualization community to get an overview of recent visualization techniques. (ii) It emphasizes and explains the necessity for further research for visualizations in this context

Low-rank Based Algorithms for Rectification, Repetition Detection and De-noising in Urban Images

In this thesis, we aim to solve the problem of automatic image rectification and repeated patterns detection on 2D urban images, using novel low-rank based techniques. Repeated patterns (such as windows, tiles, balconies and doors) are prominent and significant features in urban scenes. Detection of the periodic structures is useful in many applications such as photorealistic 3D reconstruction, 2D-to-3D alignment, facade parsing, city modeling, classification, navigation, visualization in 3D map environments, shape completion, cinematography and 3D games. However both of the image rectification and repeated patterns detection problems are challenging due to scene occlusions, varying illumination, pose variation and sensor noise. Therefore, detection of these repeated patterns becomes very important for city scene analysis. Given a 2D image of urban scene, we automatically rectify a facade image and extract facade textures first. Based on the rectified facade texture, we exploit novel algorithms that extract repeated patterns by using Kronecker product based modeling that is based on a solid theoretical foundation. We have tested our algorithms in a large set of images, which includes building facades from Paris, Hong Kong and New York

Directional edge and texture representations for image processing

An efficient representation for natural images is of fundamental importance in image processing and analysis. The commonly used separable transforms such as wavelets axe not best suited for images due to their inability to exploit directional regularities such as edges and oriented textural patterns; while most of the recently proposed directional schemes cannot represent these two types of features in a unified transform. This thesis focuses on the development of directional representations for images which can capture both edges and textures in a multiresolution manner. The thesis first considers the problem of extracting linear features with the multiresolution Fourier transform (MFT). Based on a previous MFT-based linear feature model, the work extends the extraction method into the situation when the image is corrupted by noise. The problem is tackled by the combination of a "Signal+Noise" frequency model, a refinement stage and a robust classification scheme. As a result, the MFT is able to perform linear feature analysis on noisy images on which previous methods failed. A new set of transforms called the multiscale polar cosine transforms (MPCT) are also proposed in order to represent textures. The MPCT can be regarded as real-valued MFT with similar basis functions of oriented sinusoids. It is shown that the transform can represent textural patches more efficiently than the conventional Fourier basis. With a directional best cosine basis, the MPCT packet (MPCPT) is shown to be an efficient representation for edges and textures, despite its high computational burden. The problem of representing edges and textures in a fixed transform with less complexity is then considered. This is achieved by applying a Gaussian frequency filter, which matches the disperson of the magnitude spectrum, on the local MFT coefficients. This is particularly effective in denoising natural images, due to its ability to preserve both types of feature. Further improvements can be made by employing the information given by the linear feature extraction process in the filter's configuration. The denoising results compare favourably against other state-of-the-art directional representations