Light Field compression and manipulation via residual convolutional neural network

Light field (LF) imaging has gained significant attention due to its recent success in microscopy, 3-dimensional (3D) displaying and rendering, augmented and virtual reality usage. Postprocessing of LF enables us to extract more information from a scene compared to traditional cameras. However, the use of LF is still a research novelty because of the current limitations in capturing high-resolution LF in all of its four dimensions. While researchers are actively improving methods of capturing high-resolution LF\u27s, using simulation, it is possible to explore a high-quality captured LF\u27s properties. The immediate concerns following the LF capture are its storage and processing time. A rich LF occupies a large chunk of memory ---order of multiple gigabytes per LF---. Also, most feature extraction techniques associated with LF postprocessing involve multi-dimensional integration that requires access to the whole LF and is usually time-consuming. Recent advancements in computer processing units made it possible to simulate realistic images using physical-based rendering software. In this work, at first, a transformation function is proposed for building a camera array (CA) to capture the same portion of LF from a scene that a standard plenoptic camera (SPC) can acquire. Using this transformation, LF simulation with similar properties as a plenoptic camera will become trivial in any rendering software. Artificial intelligence (AI) and machine learning (ML) algorithms ---when deployed on the new generation of GPUs--- are faster than ever. It is possible to generate and train large networks with millions of trainable parameters to learn very complex features. Here, residual convolutional neural network (RCNN) structures are employed to build complex networks for compression and feature extraction from an LF. By combining state-of-the-art image compression and RCNN, I have created a compression pipeline. The proposed pipeline\u27s bit per pixel (bpp) ratio is 0.0047 on average. I show that with a 1% compression time cost and 18x speedup for decompression, our methods reconstructed LFs have better structural similarity index metric (SSIM) and comparable peak signal-to-noise ratio (PSNR) compared to the state-of-the-art video compression techniques used to compress LFs. In the end, using RCNN, I created a network called RefNet, for extracting a group of 16 refocused images from a raw LF. The training parameters of the 16 LFs are set to (\alpha=0.125, 0.250, 0.375, ..., 2.0) for training. I show that RefNet is 134x faster than the state-of-the-art refocusing technique. The RefNet is also superior in color prediction compared to the state-of-the-art ---Fourier slice and shift-and-sum--- methods

Strategic and practical guidelines for successful structured illumination microscopy

Linear 2D- or 3D-structured illumination microscopy (SIM or3D-SIM, respectively) enables multicolor volumetric imaging of fixed and live specimens with subdiffraction resolution in all spatial dimensions. However, the reliance of SIM on algorithmic post-processing renders it particularly sensitive to artifacts that may reduce resolution, compromise data and its interpretations, and drain resources in terms of money and time spent. Here we present a protocol that allows users to generate high-quality SIM data while accounting and correcting for common artifacts. The protocol details preparation of calibration bead slides designed for SIM-based experiments, the acquisition of calibration data, the documentation of typically encountered SIM artifacts and corrective measures that should be taken to reduce them. It also includes a conceptual overview and checklist for experimental design and calibration decisions, and is applicable to any commercially available or custom platform. This protocol, plus accompanying guidelines, allows researchers from students to imaging professionals to create an optimal SIM imaging environment regardless of specimen type or structure of interest. The calibration sample preparation and system calibration protocol can be executed within 1-2 d

Image Quality Modeling and Optimization for Non-Conventional Aperture Imaging Systems

The majority of image quality studies have been performed on systems with conventional aperture functions. These systems have straightforward aperture designs and well-understood behavior. Image quality for these systems can be predicted by the General Image Quality Equation (GIQE). However, in order to continue pushing the boundaries of imaging, more control over the point spread function of an imaging system may be necessary. This requires modifications in the pupil plane of a system, causing a departure from the realm of most image quality studies. Examples include sparse apertures, synthetic apertures, coded apertures and phase elements. This work will focus on sparse aperture telescopes and the image quality issues associated with them, however, the methods presented will be applicable to other non-conventional aperture systems. \\ In this research, an approach for modeling the image quality of non-conventional aperture systems will be introduced. While the modeling approach is based in previous work, a novel validation study will be performed, which accounts for the effects of both broadband illumination and wavefront error. One of the key image quality challenges for sparse apertures is post-processing ringing artifacts. These artifacts have been observed in modeled data, but a validation study will be performed to observe them in measured data and to compare them to model predictions. Once validated, the modeling approach will be used to perform a small set of design studies for sparse aperture systems, including spectral bandpass selection and aperture layout optimization

Pre-Trained Driving in Localized Surroundings with Semantic Radar Information and Machine Learning

Entlang der Signalverarbeitungskette von Radar Detektionen bis zur Fahrzeugansteuerung, diskutiert diese Arbeit eine semantischen Radar Segmentierung, einen darauf aufbauenden Radar SLAM, sowie eine im Verbund realisierte autonome Parkfunktion. Die Radarsegmentierung der (statischen) Umgebung wird durch ein Radar-spezifisches neuronales Netzwerk RadarNet erreicht. Diese Segmentierung ermöglicht die Entwicklung des semantischen Radar Graph-SLAM SERALOC. Auf der Grundlage der semantischen Radar SLAM Karte wird eine beispielhafte autonome Parkfunktionalität in einem realen Versuchsträger umgesetzt. Entlang eines aufgezeichneten Referenzfades parkt die Funktion ausschließlich auf Basis der Radar Wahrnehmung mit bisher unerreichter Positioniergenauigkeit. Im ersten Schritt wird ein Datensatz von 8.2 · 10^6 punktweise semantisch gelabelten Radarpunktwolken über eine Strecke von 2507.35m generiert. Es sind keine vergleichbaren Datensätze dieser Annotationsebene und Radarspezifikation öffentlich verfügbar. Das überwachte Training der semantischen Segmentierung RadarNet erreicht 28.97% mIoU auf sechs Klassen. Außerdem wird ein automatisiertes Radar-Labeling-Framework SeRaLF vorgestellt, welches das Radarlabeling multimodal mittels Referenzkameras und LiDAR unterstützt. Für die kohärente Kartierung wird ein Radarsignal-Vorfilter auf der Grundlage einer Aktivierungskarte entworfen, welcher Rauschen und andere dynamische Mehrwegreflektionen unterdrückt. Ein speziell für Radar angepasstes Graph-SLAM-Frontend mit Radar-Odometrie Kanten zwischen Teil-Karten und semantisch separater NDT Registrierung setzt die vorgefilterten semantischen Radarscans zu einer konsistenten metrischen Karte zusammen. Die Kartierungsgenauigkeit und die Datenassoziation werden somit erhöht und der erste semantische Radar Graph-SLAM für beliebige statische Umgebungen realisiert. Integriert in ein reales Testfahrzeug, wird das Zusammenspiel der live RadarNet Segmentierung und des semantischen Radar Graph-SLAM anhand einer rein Radar-basierten autonomen Parkfunktionalität evaluiert. Im Durchschnitt über 42 autonome Parkmanöver (∅3.73 km/h) bei durchschnittlicher Manöverlänge von ∅172.75m wird ein Median absoluter Posenfehler von 0.235m und End-Posenfehler von 0.2443m erreicht, der vergleichbare Radar-Lokalisierungsergebnisse um ≈ 50% übertrifft. Die Kartengenauigkeit von veränderlichen, neukartierten Orten über eine Kartierungsdistanz von ∅165m ergibt eine ≈ 56%-ige Kartenkonsistenz bei einer Abweichung von ∅0.163m. Für das autonome Parken wurde ein gegebener Trajektorienplaner und Regleransatz verwendet

Computational methods for 3D imaging of neural activity in light-field microscopy

Light Field Microscopy (LFM) is a 3D imaging technique that captures spatial and angular information from light in a single snapshot. LFM is an appealing technique for applications in biological imaging due to its relatively simple implementation and fast 3D imaging speed. For instance, LFM can help to understand how neurons process information, as shown for functional neuronal calcium imaging. However, traditional volume reconstruction approaches for LFM suffer from low lateral resolution, high computational cost, and reconstruction artifacts near the native object plane. Therefore, in this thesis, we propose computational methods to improve the reconstruction performance of 3D imaging for LFM with applications to imaging neural activity. First, we study the image formation process and propose methods for discretization and simplification of the LF system. Typical approaches for discretization are performed by computing the discrete impulse response at different input locations defined by a sampling grid. Unlike conventional methods, we propose an approach that uses shift-invariant subspaces to generalize the discretization framework used in LFM. Our approach allows the selection of diverse sampling kernels and sampling intervals. Furthermore, the typical discretization method is a particular case of our formulation. Moreover, we propose a description of the system based on filter banks that fit the physics of the system. The periodic-shift invariant property per depth guarantees that the system can be accurately described by using filter banks. This description leads to a novel method to reduce the computational time using singular value decomposition (SVD). Our simplification method capitalizes on the inherent low-rank behaviour of the system. Furthermore, we propose rearranging our filter-bank model into a linear convolution neural network (CNN) that allows more convenient implementation using existing deep-learning software. Then, we study the problem of 3D reconstruction from single light-field images. We propose the shift-invariant-subspace assumption as a prior for volume reconstruction under ideal conditions. We experimentally show that artifact-free reconstruction (aliasing-free) is achievable under these settings. Furthermore, the tools developed to study the forward model are exploited to design a reconstruction algorithm based on ADMM that allows artifact-free 3D reconstruction for real data. Contrary to traditional approaches, our method includes additional priors for reconstruction without dramatically increasing the computational complexity. We extensively evaluate our approach on synthetic and real data and show that our approach performs better than conventional model-based strategies in computational time, image quality, and artifact reduction. Finally, we exploit deep-learning techniques for reconstruction. Specifically, we propose to use two-photon imaging to enhance the performance of LFM when imaging neurons in brain tissues. The architecture of our network is derived from a sparsity-based algorithm for reconstruction named Iterative Shrinkage and Thresholding Algorithm (ISTA). Furthermore, we propose a semi-supervised training based on Generative Adversarial Neural Networks (GANs) that exploits the knowledge of the forward model to achieve remarkable reconstruction quality. We propose efficient architectures to compute the forward model using linear CNNs. This description allows fast computation of the forward model and complements our reconstruction approach. Our method is tested under adverse conditions: lack of training data, background noise, and non-transparent samples. We experimentally show that our method performs better than model-based reconstruction strategies and typical neural networks for imaging neuronal activity in mammalian brain tissue. Our approach enjoys both the robustness of the model-based methods and the reconstruction speed of deep learning.Open Acces