Video and Image Super-Resolution via Deep Learning with Attention Mechanism

Image demosaicing, image super-resolution and video super-resolution are three important tasks in color imaging pipeline. Demosaicing deals with the recovery of missing color information and generation of full-resolution color images from so-called Color filter Array (CFA) such as Bayer pattern. Image super-resolution aims at increasing the spatial resolution and enhance important structures (e.g., edges and textures) in super-resolved images. Both spatial and temporal dependency are important to the task of video super-resolution, which has received increasingly more attention in recent years. Traditional solutions to these three low-level vision tasks lack generalization capability especially for real-world data. Recently, deep learning methods have achieved great success in vision problems including image demosaicing and image/video super-resolution. Conceptually similar to adaptation in model-based approaches, attention has received increasing more usage in deep learning recently. As a tool to reallocate limited computational resources based on the importance of informative components, attention mechanism which includes channel attention, spatial attention, non-local attention, etc. has found successful applications in both highlevel and low-level vision tasks. However, to the best of our knowledge, 1) most approaches independently studied super-resolution and demosaicing; little is known about the potential benefit of formulating a joint demosaicing and super-resolution (JDSR) problem; 2) attention mechanism has not been studied for spectral channels of color images in the open literature; 3) current approaches for video super-resolution implement deformable convolution based frame alignment methods and naive spatial attention mechanism. How to exploit attention mechanism in spectral and temporal domains sets up the stage for the research in this dissertation. In this dissertation, we conduct a systematic study about those two issues and make the following contributions: 1) we propose a spatial color attention network (SCAN) designed to jointly exploit the spatial and spectral dependency within color images for single image super-resolution (SISR) problem. We present a spatial color attention module that calibrates important color information for individual color components from output feature maps of residual groups. Experimental results have shown that SCAN has achieved superior performance in terms of both subjective and objective qualities on the NTIRE2019 dataset; 2) we propose two competing end-to-end joint optimization solutions to the JDSR problem: Densely-Connected Squeeze-and-Excitation Residual Network (DSERN) vs. Residual-Dense Squeeze-and-Excitation Network (RDSEN). Experimental results have shown that an enhanced design RDSEN can significantly improve both subjective and objective performance over DSERN; 3) we propose a novel deep learning based framework, Deformable Kernel Spatial Attention Network (DKSAN) to super-resolve videos with a scale factor as large as 16 (the extreme SR situation). Thanks to newly designed Deformable Kernel Convolution Alignment (DKC Align) and Deformable Kernel Spatial Attention (DKSA) modules, DKSAN can get both better subjective and objective results when compared with the existing state-of-the-art approach enhanced deformable convolutional network (EDVR)

Exploring the Internal Statistics: Single Image Super-Resolution, Completion and Captioning

Image enhancement has drawn increasingly attention in improving image quality or interpretability. It aims to modify images to achieve a better perception for human visual system or a more suitable representation for further analysis in a variety of applications such as medical imaging, remote sensing, and video surveillance. Based on different attributes of the given input images, enhancement tasks vary, e.g., noise removal, deblurring, resolution enhancement, prediction of missing pixels, etc. The latter two are usually referred to as image super-resolution and image inpainting (or completion). Image super-resolution and completion are numerically ill-posed problems. Multi-frame-based approaches make use of the presence of aliasing in multiple frames of the same scene. For cases where only one input image is available, it is extremely challenging to estimate the unknown pixel values. In this dissertation, we target at single image super-resolution and completion by exploring the internal statistics within the input image and across scales. An internal gradient similarity-based single image super-resolution algorithm is first presented. Then we demonstrate that the proposed framework could be naturally extended to accomplish super-resolution and completion simultaneously. Afterwards, a hybrid learning-based single image super-resolution approach is proposed to benefit from both external and internal statistics. This framework hinges on image-level hallucination from externally learned regression models as well as gradient level pyramid self-awareness for edges and textures refinement. The framework is then employed to break the resolution limitation of the passive microwave imagery and to boost the tracking accuracy of the sea ice movements. To extend our research to the quality enhancement of the depth maps, a novel system is presented to handle circumstances where only one pair of registered low-resolution intensity and depth images are available. High quality RGB and depth images are generated after the system. Extensive experimental results have demonstrated the effectiveness of all the proposed frameworks both quantitatively and qualitatively. Different from image super-resolution and completion which belong to low-level vision research, image captioning is a high-level vision task related to the semantic understanding of an input image. It is a natural task for human beings. However, image captioning remains challenging from a computer vision point of view especially due to the fact that the task itself is ambiguous. In principle, descriptions of an image can talk about any visual aspects in it varying from object attributes to scene features, or even refer to objects that are not depicted and the hidden interaction or connection that requires common sense knowledge to analyze. Therefore, learning-based image captioning is in general a data-driven task, which relies on the training dataset. Descriptions in the majority of the existing image-sentence datasets are generated by humans under specific instructions. Real-world sentence data is rarely directly utilized for training since it is sometimes noisy and unbalanced, which makes it ‘imperfect’ for the training of the image captioning task. In this dissertation, we present a novel image captioning framework to deal with the uncontrolled image-sentence dataset where descriptions could be strongly or weakly correlated to the image content and in arbitrary lengths. A self-guiding learning process is proposed to fully reveal the internal statistics of the training dataset and to look into the learning process in a global way and generate descriptions that are syntactically correct and semantically sound

Content-Aware Image Restoration Techniques without Ground Truth and Novel Ideas to Image Reconstruction

In this thesis I will use state-of-the-art (SOTA) image denoising methods to denoise electron microscopy (EM) data. Then, I will present NoiseVoid a deep learning based self-supervised image denoising approach which is trained on single noisy observations. Eventually, I approach the missing wedge problem in tomography and introduce a novel image encoding, based on the Fourier transform which I am using to predict missing Fourier coefficients directly in Fourier space with Fourier Image Transformer (FIT). In the next paragraphs I will summarize the individual contributions briefly. Electron microscopy is the go to method for high-resolution images in biological research. Modern scanning electron microscopy (SEM) setups are used to obtain neural connectivity maps, allowing us to identify individual synapses. However, slow scanning speeds are required to obtain SEM images of sufficient quality. In (Weigert et al. 2018) the authors show, for fluorescence microscopy, how pairs of low- and high-quality images can be obtained from biological samples and use them to train content-aware image restoration (CARE) networks. Once such a network is trained, it can be applied to noisy data to restore high quality images. With SEM-CARE I present how this approach can be directly applied to SEM data, allowing us to scan the samples faster, resulting in $40$- to $50$-fold imaging speedups for SEM imaging. In structural biology cryo transmission electron microscopy (cryo TEM) is used to resolve protein structures and describe molecular interactions. However, missing contrast agents as well as beam induced sample damage (Knapek and Dubochet 1980) prevent acquisition of high quality projection images. Hence, reconstructed tomograms suffer from low signal-to-noise ratio (SNR) and low contrast, which makes post-processing of such data difficult and often has to be done manually. To facilitate down stream analysis and manual data browsing of cryo tomograms I present cryoCARE a Noise2Noise (Lehtinen et al. 2018) based denoising method which is able to restore high contrast, low noise tomograms from sparse-view low-dose tilt-series. An implementation of cryoCARE is publicly available as Scipion (de la Rosa-Trevín et al. 2016) plugin. Next, I will discuss the problem of self-supervised image denoising. With cryoCARE I exploited the fact that modern cryo TEM cameras acquire multiple low-dose images, hence the Noise2Noise (Lehtinen et al. 2018) training paradigm can be applied. However, acquiring multiple noisy observations is not always possible e.g. in live imaging, with old cryo TEM cameras or simply by lack of access to the used imaging system. In such cases we have to fall back to self-supervised denoising methods and with Noise2Void I present the first self-supervised neural network based image denoising approach. Noise2Void is also available as an open-source Python package and as a one-click solution in Fiji (Schindelin et al. 2012). In the last part of this thesis I present Fourier Image Transformer (FIT) a novel approach to image reconstruction with Transformer networks. I develop a novel 1D image encoding based on the Fourier transform where each prefix encodes the whole image at reduced resolution, which I call Fourier Domain Encoding (FDE). I use FIT with FDEs and present proof of concept for super-resolution and tomographic reconstruction with missing wedge correction. The missing wedge artefacts in tomographic imaging originate in sparse-view imaging. Sparse-view imaging is used to keep the total exposure of the imaged sample to a minimum, by only acquiring a limited number of projection images. However, tomographic reconstructions from sparse-view acquisitions are affected by missing wedge artefacts, characterized by missing wedges in the Fourier space and visible as streaking artefacts in real image space. I show that FITs can be applied to tomographic reconstruction and that they fill in missing Fourier coefficients. Hence, FIT for tomographic reconstruction solves the missing wedge problem at its source.:Contents Summary iii Acknowledgements v 1 Introduction 1 1.1 Scanning Electron Microscopy . . . . . . . . . . . . . . . . . . . . 3 1.2 Cryo Transmission Electron Microscopy . . . . . . . . . . . . . . . 4 1.2.1 Single Particle Analysis . . . . . . . . . . . . . . . . . . . . 5 1.2.2 Cryo Tomography . . . . . . . . . . . . . . . . . . . . . . . 7 1.3 Tomographic Reconstruction . . . . . . . . . . . . . . . . . . . . . 8 1.4 Overview and Contributions . . . . . . . . . . . . . . . . . . . . . 11 2 Denoising in Electron Microscopy 15 2.1 Image Denoising . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2.2 Supervised Image Restoration . . . . . . . . . . . . . . . . . . . . 19 2.2.1 Training and Validation Loss . . . . . . . . . . . . . . . . 19 2.2.2 Neural Network Architectures . . . . . . . . . . . . . . . . 21 2.3 SEM-CARE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 2.3.1 SEM-CARE Experiments . . . . . . . . . . . . . . . . . . 23 2.3.2 SEM-CARE Results . . . . . . . . . . . . . . . . . . . . . 25 2.4 Noise2Noise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 2.5 cryoCARE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 2.5.1 Restoration of cryo TEM Projections . . . . . . . . . . . . 27 2.5.2 Restoration of cryo TEM Tomograms . . . . . . . . . . . . 29 2.5.3 Automated Downstream Analysis . . . . . . . . . . . . . . 31 2.6 Implementations and Availability . . . . . . . . . . . . . . . . . . 32 2.7 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 2.7.1 Tasks Facilitated through cryoCARE . . . . . . . . . . . 33 3 Noise2Void: Self-Supervised Denoising 35 3.1 Probabilistic Image Formation . . . . . . . . . . . . . . . . . . . . 37 3.2 Receptive Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3.3 Noise2Void Training . . . . . . . . . . . . . . . . . . . . . . . . . 39 3.3.1 Implementation Details . . . . . . . . . . . . . . . . . . . . 41 3.4 Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 3.4.1 Natural Images . . . . . . . . . . . . . . . . . . . . . . . . 43 3.4.2 Light Microscopy Data . . . . . . . . . . . . . . . . . . . . 44 3.4.3 Electron Microscopy Data . . . . . . . . . . . . . . . . . . 47 3.4.4 Errors and Limitations . . . . . . . . . . . . . . . . . . . . 48 3.5 Conclusion and Followup Work . . . . . . . . . . . . . . . . . . . 50 4 Fourier Image Transformer 53 4.1 Transformers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 4.1.1 Attention Is All You Need . . . . . . . . . . . . . . . . . . 55 4.1.2 Fast-Transformers . . . . . . . . . . . . . . . . . . . . . . . 56 4.1.3 Transformers in Computer Vision . . . . . . . . . . . . . . 57 4.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 4.2.1 Fourier Domain Encodings (FDEs) . . . . . . . . . . . . . 57 4.2.2 Fourier Coefficient Loss . . . . . . . . . . . . . . . . . . . . 59 4.3 FIT for Super-Resolution . . . . . . . . . . . . . . . . . . . . . . . 60 4.3.1 Super-Resolution Data . . . . . . . . . . . . . . . . . . . . 60 4.3.2 Super-Resolution Experiments . . . . . . . . . . . . . . . . 61 4.4 FIT for Tomography . . . . . . . . . . . . . . . . . . . . . . . . . 63 4.4.1 Computed Tomography Data . . . . . . . . . . . . . . . . 64 4.4.2 Computed Tomography Experiments . . . . . . . . . . . . 66 4.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 5 Conclusions and Outlook 7