Approach to Super-Resolution Through the Concept of Multicamera Imaging

Super-resolution consists of processing an image or a set of images in order to enhance the resolution of a video sequence or a single frame. There are several methods to apply super-resolution, from which fusion super-resolution techniques are considered to be the most adequate for real-time implementations. In fusion, super-resolution and high-resolution images are constructed from several observed low-resolution images, thereby increasing the high-frequency components and removing the degradations caused by the recording process of low-resolution imaging acquisition devices. Moreover, the proposed imaging system considered in this work is based on capturing various frames from several sensors, which are attached to one another by a P × Q array. This framework is known as a multicamera system. This chapter summarizes the research conducted to apply fusion super-resolution techniques to select the most adequate frames and macroblocks together with a multicamera array. This approach optimizes the temporal and spatial correlations in the frames and reduces as a consequence the appearance of annoying artifacts, enhancing the quality of the processed high-resolution sequence and minimizing the execution time

A multi-camera approach to image-based rendering and 3-D/Multiview display of ancient chinese artifacts

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Bioimage informatics in STED super-resolution microscopy

Optical microscopy is living its renaissance. The diffraction limit, although still physically true, plays a minor role in the achievable resolution in far-field fluorescence microscopy. Super-resolution techniques enable fluorescence microscopy at nearly molecular resolution. Modern (super-resolution) microscopy methods rely strongly on software. Software tools are needed all the way from data acquisition, data storage, image reconstruction, restoration and alignment, to quantitative image analysis and image visualization. These tools play a key role in all aspects of microscopy today – and their importance in the coming years is certainly going to increase, when microscopy little-by-little transitions from single cells into more complex and even living model systems. In this thesis, a series of bioimage informatics software tools are introduced for STED super-resolution microscopy. Tomographic reconstruction software, coupled with a novel image acquisition method STED< is shown to enable axial (3D) super-resolution imaging in a standard 2D-STED microscope. Software tools are introduced for STED super-resolution correlative imaging with transmission electron microscopes or atomic force microscopes. A novel method for automatically ranking image quality within microscope image datasets is introduced, and it is utilized to for example select the best images in a STED microscope image dataset.Siirretty Doriast

From nanometers to centimeters: Imaging across spatial scales with smart computer-aided microscopy

Microscopes have been an invaluable tool throughout the history of the life sciences, as they allow researchers to observe the miniscule details of living systems in space and time. However, modern biology studies complex and non-obvious phenotypes and their distributions in populations and thus requires that microscopes evolve from visual aids for anecdotal observation into instruments for objective and quantitative measurements. To this end, many cutting-edge developments in microscopy are fuelled by innovations in the computational processing of the generated images. Computational tools can be applied in the early stages of an experiment, where they allow for reconstruction of images with higher resolution and contrast or more colors compared to raw data. In the final analysis stage, state-of-the-art image analysis pipelines seek to extract interpretable and humanly tractable information from the high-dimensional space of images. In the work presented in this thesis, I performed super-resolution microscopy and wrote image analysis pipelines to derive quantitative information about multiple biological processes. I contributed to studies on the regulation of DNMT1 by implementing machine learning-based segmentation of replication sites in images and performed quantitative statistical analysis of the recruitment of multiple DNMT1 mutants. To study the spatiotemporal distribution of DNA damage response I performed STED microscopy and could provide a lower bound on the size of the elementary spatial units of DNA repair. In this project, I also wrote image analysis pipelines and performed statistical analysis to show a decoupling of DNA density and heterochromatin marks during repair. More on the experimental side, I helped in the establishment of a protocol for many-fold color multiplexing by iterative labelling of diverse structures via DNA hybridization. Turning from small scale details to the distribution of phenotypes in a population, I wrote a reusable pipeline for fitting models of cell cycle stage distribution and inhibition curves to high-throughput measurements to quickly quantify the effects of innovative antiproliferative antibody-drug-conjugates. The main focus of the thesis is BigStitcher, a tool for the management and alignment of terabyte-sized image datasets. Such enormous datasets are nowadays generated routinely with light-sheet microscopy and sample preparation techniques such as clearing or expansion. Their sheer size, high dimensionality and unique optical properties poses a serious bottleneck for researchers and requires specialized processing tools, as the images often do not fit into the main memory of most computers. BigStitcher primarily allows for fast registration of such many-dimensional datasets on conventional hardware using optimized multi-resolution alignment algorithms. The software can also correct a variety of aberrations such as fixed-pattern noise, chromatic shifts and even complex sample-induced distortions. A defining feature of BigStitcher, as well as the various image analysis scripts developed in this work is their interactivity. A central goal was to leverage the user's expertise at key moments and bring innovations from the big data world to the lab with its smaller and much more diverse datasets without replacing scientists with automated black-box pipelines. To this end, BigStitcher was implemented as a user-friendly plug-in for the open source image processing platform Fiji and provides the users with a nearly instantaneous preview of the aligned images and opportunities for manual control of all processing steps. With its powerful features and ease-of-use, BigStitcher paves the way to the routine application of light-sheet microscopy and other methods producing equally large datasets

Compression and Subjective Quality Assessment of 3D Video

In recent years, three-dimensional television (3D TV) has been broadly considered as the successor to the existing traditional two-dimensional television (2D TV) sets. With its capability of offering a dynamic and immersive experience, 3D video (3DV) is expected to expand conventional video in several applications in the near future. However, 3D content requires more than a single view to deliver the depth sensation to the viewers and this, inevitably, increases the bitrate compared to the corresponding 2D content. This need drives the research trend in video compression field towards more advanced and more efficient algorithms. Currently, the Advanced Video Coding (H.264/AVC) is the state-of-the-art video coding standard which has been developed by the Joint Video Team of ISO/IEC MPEG and ITU-T VCEG. This codec has been widely adopted in various applications and products such as TV broadcasting, video conferencing, mobile TV, and blue-ray disc. One important extension of H.264/AVC, namely Multiview Video Coding (MVC) was an attempt to multiple view compression by taking into consideration the inter-view dependency between different views of the same scene. This codec H.264/AVC with its MVC extension (H.264/MVC) can be used for encoding either conventional stereoscopic video, including only two views, or multiview video, including more than two views. In spite of the high performance of H.264/MVC, a typical multiview video sequence requires a huge amount of storage space, which is proportional to the number of offered views. The available views are still limited and the research has been devoted to synthesizing an arbitrary number of views using the multiview video and depth map (MVD). This process is mandatory for auto-stereoscopic displays (ASDs) where many views are required at the viewer side and there is no way to transmit such a relatively huge number of views with currently available broadcasting technology. Therefore, to satisfy the growing hunger for 3D related applications, it is mandatory to further decrease the bitstream by introducing new and more efficient algorithms for compressing multiview video and depth maps. This thesis tackles the 3D content compression targeting different formats i.e. stereoscopic video and depth-enhanced multiview video. Stereoscopic video compression algorithms introduced in this thesis mostly focus on proposing different types of asymmetry between the left and right views. This means reducing the quality of one view compared to the other view aiming to achieve a better subjective quality against the symmetric case (the reference) and under the same bitrate constraint. The proposed algorithms to optimize depth-enhanced multiview video compression include both texture compression schemes as well as depth map coding tools. Some of the introduced coding schemes proposed for this format include asymmetric quality between the views. Knowing that objective metrics are not able to accurately estimate the subjective quality of stereoscopic content, it is suggested to perform subjective quality assessment to evaluate different codecs. Moreover, when the concept of asymmetry is introduced, the Human Visual System (HVS) performs a fusion process which is not completely understood. Therefore, another important aspect of this thesis is conducting several subjective tests and reporting the subjective ratings to evaluate the perceived quality of the proposed coded content against the references. Statistical analysis is carried out in the thesis to assess the validity of the subjective ratings and determine the best performing test cases

Super Resolution of Wavelet-Encoded Images and Videos

In this dissertation, we address the multiframe super resolution reconstruction problem for wavelet-encoded images and videos. The goal of multiframe super resolution is to obtain one or more high resolution images by fusing a sequence of degraded or aliased low resolution images of the same scene. Since the low resolution images may be unaligned, a registration step is required before super resolution reconstruction. Therefore, we first explore in-band (i.e. in the wavelet-domain) image registration; then, investigate super resolution. Our motivation for analyzing the image registration and super resolution problems in the wavelet domain is the growing trend in wavelet-encoded imaging, and wavelet-encoding for image/video compression. Due to drawbacks of widely used discrete cosine transform in image and video compression, a considerable amount of literature is devoted to wavelet-based methods. However, since wavelets are shift-variant, existing methods cannot utilize wavelet subbands efficiently. In order to overcome this drawback, we establish and explore the direct relationship between the subbands under a translational shift, for image registration and super resolution. We then employ our devised in-band methodology, in a motion compensated video compression framework, to demonstrate the effective usage of wavelet subbands. Super resolution can also be used as a post-processing step in video compression in order to decrease the size of the video files to be compressed, with downsampling added as a pre-processing step. Therefore, we present a video compression scheme that utilizes super resolution to reconstruct the high frequency information lost during downsampling. In addition, super resolution is a crucial post-processing step for satellite imagery, due to the fact that it is hard to update imaging devices after a satellite is launched. Thus, we also demonstrate the usage of our devised methods in enhancing resolution of pansharpened multispectral images

From nanometers to centimeters: Imaging across spatial scales with smart computer-aided microscopy

Microscopes have been an invaluable tool throughout the history of the life sciences, as they allow researchers to observe the miniscule details of living systems in space and time. However, modern biology studies complex and non-obvious phenotypes and their distributions in populations and thus requires that microscopes evolve from visual aids for anecdotal observation into instruments for objective and quantitative measurements. To this end, many cutting-edge developments in microscopy are fuelled by innovations in the computational processing of the generated images. Computational tools can be applied in the early stages of an experiment, where they allow for reconstruction of images with higher resolution and contrast or more colors compared to raw data. In the final analysis stage, state-of-the-art image analysis pipelines seek to extract interpretable and humanly tractable information from the high-dimensional space of images. In the work presented in this thesis, I performed super-resolution microscopy and wrote image analysis pipelines to derive quantitative information about multiple biological processes. I contributed to studies on the regulation of DNMT1 by implementing machine learning-based segmentation of replication sites in images and performed quantitative statistical analysis of the recruitment of multiple DNMT1 mutants. To study the spatiotemporal distribution of DNA damage response I performed STED microscopy and could provide a lower bound on the size of the elementary spatial units of DNA repair. In this project, I also wrote image analysis pipelines and performed statistical analysis to show a decoupling of DNA density and heterochromatin marks during repair. More on the experimental side, I helped in the establishment of a protocol for many-fold color multiplexing by iterative labelling of diverse structures via DNA hybridization. Turning from small scale details to the distribution of phenotypes in a population, I wrote a reusable pipeline for fitting models of cell cycle stage distribution and inhibition curves to high-throughput measurements to quickly quantify the effects of innovative antiproliferative antibody-drug-conjugates. The main focus of the thesis is BigStitcher, a tool for the management and alignment of terabyte-sized image datasets. Such enormous datasets are nowadays generated routinely with light-sheet microscopy and sample preparation techniques such as clearing or expansion. Their sheer size, high dimensionality and unique optical properties poses a serious bottleneck for researchers and requires specialized processing tools, as the images often do not fit into the main memory of most computers. BigStitcher primarily allows for fast registration of such many-dimensional datasets on conventional hardware using optimized multi-resolution alignment algorithms. The software can also correct a variety of aberrations such as fixed-pattern noise, chromatic shifts and even complex sample-induced distortions. A defining feature of BigStitcher, as well as the various image analysis scripts developed in this work is their interactivity. A central goal was to leverage the user's expertise at key moments and bring innovations from the big data world to the lab with its smaller and much more diverse datasets without replacing scientists with automated black-box pipelines. To this end, BigStitcher was implemented as a user-friendly plug-in for the open source image processing platform Fiji and provides the users with a nearly instantaneous preview of the aligned images and opportunities for manual control of all processing steps. With its powerful features and ease-of-use, BigStitcher paves the way to the routine application of light-sheet microscopy and other methods producing equally large datasets

Transport-Based Neural Style Transfer for Smoke Simulations

Artistically controlling fluids has always been a challenging task. Optimization techniques rely on approximating simulation states towards target velocity or density field configurations, which are often handcrafted by artists to indirectly control smoke dynamics. Patch synthesis techniques transfer image textures or simulation features to a target flow field. However, these are either limited to adding structural patterns or augmenting coarse flows with turbulent structures, and hence cannot capture the full spectrum of different styles and semantically complex structures. In this paper, we propose the first Transport-based Neural Style Transfer (TNST) algorithm for volumetric smoke data. Our method is able to transfer features from natural images to smoke simulations, enabling general content-aware manipulations ranging from simple patterns to intricate motifs. The proposed algorithm is physically inspired, since it computes the density transport from a source input smoke to a desired target configuration. Our transport-based approach allows direct control over the divergence of the stylization velocity field by optimizing incompressible and irrotational potentials that transport smoke towards stylization. Temporal consistency is ensured by transporting and aligning subsequent stylized velocities, and 3D reconstructions are computed by seamlessly merging stylizations from different camera viewpoints.Comment: ACM Transaction on Graphics (SIGGRAPH ASIA 2019), additional materials: http://www.byungsoo.me/project/neural-flow-styl

Camera positioning for 3D panoramic image rendering

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University London.Virtual camera realisation and the proposition of trapezoidal camera architecture are the two broad contributions of this thesis. Firstly, multiple camera and their arrangement constitute a critical component which affect the integrity of visual content acquisition for multi-view video. Currently, linear, convergence, and divergence arrays are the prominent camera topologies adopted. However, the large number of cameras required and their synchronisation are two of prominent challenges usually encountered. The use of virtual cameras can significantly reduce the number of physical cameras used with respect to any of the known camera structures, hence adequately reducing some of the other implementation issues. This thesis explores to use image-based rendering with and without geometry in the implementations leading to the realisation of virtual cameras. The virtual camera implementation was carried out from the perspective of depth map (geometry) and use of multiple image samples (no geometry). Prior to the virtual camera realisation, the generation of depth map was investigated using region match measures widely known for solving image point correspondence problem. The constructed depth maps have been compare with the ones generated using the dynamic programming approach. In both the geometry and no geometry approaches, the virtual cameras lead to the rendering of views from a textured depth map, construction of 3D panoramic image of a scene by stitching multiple image samples and performing superposition on them, and computation of virtual scene from a stereo pair of panoramic images. The quality of these rendered images were assessed through the use of either objective or subjective analysis in Imatest software. Further more, metric reconstruction of a scene was performed by re-projection of the pixel points from multiple image samples with a single centre of projection. This was done using sparse bundle adjustment algorithm. The statistical summary obtained after the application of this algorithm provides a gauge for the efficiency of the optimisation step. The optimised data was then visualised in Meshlab software environment, hence providing the reconstructed scene. Secondly, with any of the well-established camera arrangements, all cameras are usually constrained to the same horizontal plane. Therefore, occlusion becomes an extremely challenging problem, and a robust camera set-up is required in order to resolve strongly the hidden part of any scene objects. To adequately meet the visibility condition for scene objects and given that occlusion of the same scene objects can occur, a multi-plane camera structure is highly desirable. Therefore, this thesis also explore trapezoidal camera structure for image acquisition. The approach here is to assess the feasibility and potential of several physical cameras of the same model being sparsely arranged on the edge of an efficient trapezoid graph. This is implemented both Matlab and Maya. The quality of the depth maps rendered in Matlab are better in Quality