Improving SLI Performance in Optically Challenging Environments

The construction of 3D models of real-world scenes using non-contact methods is an important problem in computer vision. Some of the more successful methods belong to a class of techniques called structured light illumination (SLI). While SLI methods are generally very successful, there are cases where their performance is poor. Examples include scenes with a high dynamic range in albedo or scenes with strong interreflections. These scenes are referred to as optically challenging environments. The work in this dissertation is aimed at improving SLI performance in optically challenging environments. A new method of high dynamic range imaging (HDRI) based on pixel-by-pixel Kalman filtering is developed. Using objective metrics, it is show to achieve as much as a 9.4 dB improvement in signal-to-noise ratio and as much as a 29% improvement in radiometric accuracy over a classic method. Quality checks are developed to detect and quantify multipath interference and other quality defects using phase measuring profilometry (PMP). Techniques are established to improve SLI performance in the presence of strong interreflections. Approaches in compressed sensing are applied to SLI, and interreflections in a scene are modeled using SLI. Several different applications of this research are also discussed

Lucky Imaging Adaptive Optics of the brown dwarf binary GJ569Bab

The potential of combining Adaptive Optics (AO) and Lucky Imaging (LI) to achieve high precision astrometry and differential photometry in the optical is investigated by conducting observations of the close 0\farcs1 brown dwarf binary GJ569Bab. We took 50000 $I$-band images with our LI instrument FastCam attached to NAOMI, the 4.2-m William Herschel Telescope (WHT) AO facility. In order to extract the most of the astrometry and photometry of the GJ569Bab system we have resorted to a PSF fitting technique using the primary star GJ569A as a suitable PSF reference which exhibits an $I$-band magnitude of $7.78\pm0.03$. The AO+LI observations at WHT were able to resolve the binary system GJ569Bab located at 4\farcs 92 \pm 0\farcs05 from GJ569A. We measure a separation of $98.4 \pm 1.1$ mas and $I$-band magnitudes of $13.86 \pm 0.03$ and $14.48 \pm 0.03$ and $I-J$ colors of 2.72$\pm$0.08 and 2.83$\pm$0.08 for the Ba and Bb components, respectively. Our study rules out the presence of any other companion to GJ569A down to magnitude I$\sim$ 17 at distances larger than 1\arcsec. The $I-J$ colors measured are consistent with M8.5-M9 spectral types for the Ba and Bb components. The available dynamical, photometric and spectroscopic data are consistent with a binary system with Ba being slightly (10-20%) more massive than Bb. We obtain new orbital parameters which are in good agreement with those in the literature.Comment: 13 pages, 9 figures, 7 tables, in press in MNRA

Removing striping artifacts in light-sheet fluorescence microscopy: a review

In recent years, light-sheet fluorescence microscopy (LSFM) has found a broad application for imaging of diverse biological samples, ranging from sub-cellular structures to whole animals, both in-vivo and ex-vivo, owing to its many advantages relative to point-scanning methods. By providing the selective illumination of sample single planes, LSFM achieves an intrinsic optical sectioning and direct 2D image acquisition, with low out-of-focus fluorescence background, sample photo-damage and photo-bleaching. On the other hand, such an illumination scheme is prone to light absorption or scattering effects, which lead to uneven illumination and striping artifacts in the images, oriented along the light sheet propagation direction. Several methods have been developed to address this issue, ranging from fully optical solutions to entirely digital post-processing approaches. In this work, we present them, outlining their advantages, performance and limitations

Removing striping artifacts in light-sheet fluorescence microscopy: a review

In recent years, light-sheet fluorescence microscopy (LSFM) has found a broad application for imaging of diverse biological samples, ranging from sub-cellular structures to whole animals, both in-vivo and ex-vivo, owing to its many advantages relative to point-scanning methods. By providing the selective illumination of sample single planes, LSFM achieves an intrinsic optical sectioning and direct 2D image acquisition, with low out-of-focus fluorescence background, sample photo-damage and photo-bleaching. On the other hand, such an illumination scheme is prone to light absorption or scattering effects, which lead to uneven illumination and striping artifacts in the images, oriented along the light sheet propagation direction. Several methods have been developed to address this issue, ranging from fully optical solutions to entirely digital post-processing approaches. In this work, we present them, outlining their advantages, performance and limitations

Advanced image processing techniques for detection and quantification of drusen

Dissertation presented to obtain the degree of Doctor of Philosophy in Electrical Engineering, speciality on Perceptional Systems, by the Universidade Nova de Lisboa, Faculty of Sciences and TechnologyDrusen are common features in the ageing macula, caused by accumulation of extracellular materials beneath the retinal surface, visible in retinal fundus images as yellow spots. In the ophthalmologists’ opinion, the evaluation of the total drusen area, in a sequence of images taken during a treatment, will help to understand the disease progression and effectiveness. However, this evaluation is fastidious and difficult to reproduce when performed manually. A literature review on automated drusen detection showed that the works already published were limited to techniques of either adaptive or global thresholds which showed a tendency to produce a significant number of false positives. The purpose for this work was to propose an alternative method to automatically quantify drusen using advanced digital image processing techniques. This methodology is based on a detection and modelling algorithm to automatically quantify drusen. It includes an image pre-processing step to correct the uneven illumination by using smoothing splines fitting and to normalize the contrast. To quantify drusen a detection and modelling algorithm is adopted. The detection uses a new gradient based segmentation algorithm that isolates drusen and provides basic drusen characterization to the modelling stage. These are then fitted by Gaussian functions, to produce a model of the image, which is used to compute the affected areas. To validate the methodology, two software applications, one for semi-automated (MD3RI) and other for automated detection of drusen (AD3RI), were implemented. The first was developed for Ophthalmologists to manually analyse and mark drusen deposits, while the other implemented algorithms for automatic drusen quantification.Four studies to assess the methodology accuracy involving twelve specialists have taken place. These compared the automated method to the specialists and evaluated its repeatability. The studies were analysed regarding several indicators, which were based on the total affected area and on a pixel-to-pixel analysis. Due to the high variability among the graders involved in the first study, a new evaluation method, the Weighed Matching Analysis, was developed to improve the pixel-to-pixel analysis by using the statistical significance of the observations to differentiate positive and negative pixels. From the results of these studies it was concluded that the methodology proposed is capable to automatically measure drusen in an accurate and reproducible process. Also, the thesis proposes new image processing algorithms, for image pre-processing, image segmentation,image modelling and images comparison, which are also applicable to other image processing fields

Vicarious Methodologies to Assess and Improve the Quality of the Optical Remote Sensing Images: A Critical Review

Over the past decade, number of optical Earth observing satellites performing remote sensing has increased substantially, dramatically increasing the capability to monitor the Earth. The quantity of remote sensing satellite increase is primarily driven by improved technology, miniaturization of components, reduced manufacturing, and launch cost. These satellites often lack on-board calibrators that a large satellite utilizes to ensure high quality (e.g., radiometric, geometric, spatial quality, etc.) scientific measurement. To address this issue, this work presents “best” vicarious image quality assessment and improvement techniques for those kinds of optical satellites which lacks on-board calibration system. In this article, image quality categories have been explored, and essential quality parameters (e.g., absolute and relative calibration, aliasing, etc.) have been identified. For each of the parameters, appropriate characterization methods are identified along with its specifications or requirements. In cases of multiple methods, recommendation has been made based-on the strengths and weaknesses of each method. Furthermore, processing steps have been presented, including examples. Essentially, this paper provides a comprehensive study of the criteria that needs to be assessed to evaluate remote sensing satellite data quality, and best vicarious methodologies to evaluate identified quality parameters such as coherent noise, ground sample distance, etc

In-situ crack and keyhole pore detection in laser directed energy deposition through acoustic signal and deep learning

Cracks and keyhole pores are detrimental defects in alloys produced by laser directed energy deposition (LDED). Laser-material interaction sound may hold information about underlying complex physical events such as crack propagation and pores formation. However, due to the noisy environment and intricate signal content, acoustic-based monitoring in LDED has received little attention. This paper proposes a novel acoustic-based in-situ defect detection strategy in LDED. The key contribution of this study is to develop an in-situ acoustic signal denoising, feature extraction, and sound classification pipeline that incorporates convolutional neural networks (CNN) for online defect prediction. Microscope images are used to identify locations of the cracks and keyhole pores within a part. The defect locations are spatiotemporally registered with acoustic signal. Various acoustic features corresponding to defect-free regions, cracks, and keyhole pores are extracted and analysed in time-domain, frequency-domain, and time-frequency representations. The CNN model is trained to predict defect occurrences using the Mel-Frequency Cepstral Coefficients (MFCCs) of the lasermaterial interaction sound. The CNN model is compared to various classic machine learning models trained on the denoised acoustic dataset and raw acoustic dataset. The validation results shows that the CNN model trained on the denoised dataset outperforms others with the highest overall accuracy (89%), keyhole pore prediction accuracy (93%), and AUC-ROC score (98%). Furthermore, the trained CNN model can be deployed into an in-house developed software platform for online quality monitoring. The proposed strategy is the first study to use acoustic signals with deep learning for insitu defect detection in LDED process.Comment: 36 Pages, 16 Figures, accepted at journal Additive Manufacturin

Image Restoration for Remote Sensing: Overview and Toolbox

Remote sensing provides valuable information about objects or areas from a distance in either active (e.g., RADAR and LiDAR) or passive (e.g., multispectral and hyperspectral) modes. The quality of data acquired by remotely sensed imaging sensors (both active and passive) is often degraded by a variety of noise types and artifacts. Image restoration, which is a vibrant field of research in the remote sensing community, is the task of recovering the true unknown image from the degraded observed image. Each imaging sensor induces unique noise types and artifacts into the observed image. This fact has led to the expansion of restoration techniques in different paths according to each sensor type. This review paper brings together the advances of image restoration techniques with particular focuses on synthetic aperture radar and hyperspectral images as the most active sub-fields of image restoration in the remote sensing community. We, therefore, provide a comprehensive, discipline-specific starting point for researchers at different levels (i.e., students, researchers, and senior researchers) willing to investigate the vibrant topic of data restoration by supplying sufficient detail and references. Additionally, this review paper accompanies a toolbox to provide a platform to encourage interested students and researchers in the field to further explore the restoration techniques and fast-forward the community. The toolboxes are provided in https://github.com/ImageRestorationToolbox.Comment: This paper is under review in GRS

New algorithms for the analysis of live-cell images acquired in phase contrast microscopy

La détection et la caractérisation automatisée des cellules constituent un enjeu important dans de nombreux domaines de recherche tels que la cicatrisation, le développement de l'embryon et des cellules souches, l’immunologie, l’oncologie, l'ingénierie tissulaire et la découverte de nouveaux médicaments. Étudier le comportement cellulaire in vitro par imagerie des cellules vivantes et par le criblage à haut débit implique des milliers d'images et de vastes quantités de données. Des outils d'analyse automatisés reposant sur la vision numérique et les méthodes non-intrusives telles que la microscopie à contraste de phase (PCM) sont nécessaires. Comme les images PCM sont difficiles à analyser en raison du halo lumineux entourant les cellules et de la difficulté à distinguer les cellules individuelles, le but de ce projet était de développer des algorithmes de traitement d'image PCM dans Matlab® afin d’en tirer de l’information reliée à la morphologie cellulaire de manière automatisée. Pour développer ces algorithmes, des séries d’images de myoblastes acquises en PCM ont été générées, en faisant croître les cellules dans un milieu avec sérum bovin (SSM) ou dans un milieu sans sérum (SFM) sur plusieurs passages. La surface recouverte par les cellules a été estimée en utilisant un filtre de plage de valeurs, un seuil et une taille minimale de coupe afin d'examiner la cinétique de croissance cellulaire. Les résultats ont montré que les cellules avaient des taux de croissance similaires pour les deux milieux de culture, mais que celui-ci diminue de façon linéaire avec le nombre de passages. La méthode de transformée par ondelette continue combinée à l’analyse d'image multivariée (UWT-MIA) a été élaborée afin d’estimer la distribution de caractéristiques morphologiques des cellules (axe majeur, axe mineur, orientation et rondeur). Une analyse multivariée réalisée sur l’ensemble de la base de données (environ 1 million d’images PCM) a montré d'une manière quantitative que les myoblastes cultivés dans le milieu SFM étaient plus allongés et plus petits que ceux cultivés dans le milieu SSM. Les algorithmes développés grâce à ce projet pourraient être utilisés sur d'autres phénotypes cellulaires pour des applications de criblage à haut débit et de contrôle de cultures cellulaires.Automated cell detection and characterization is important in many research fields such as wound healing, embryo development, immune system studies, cancer research, parasite spreading, tissue engineering, stem cell research and drug research and testing. Studying in vitro cellular behavior via live-cell imaging and high-throughput screening involves thousands of images and vast amounts of data, and automated analysis tools relying on machine vision methods and non-intrusive methods such as phase contrast microscopy (PCM) are a necessity. However, there are still some challenges to overcome, since PCM images are difficult to analyze because of the bright halo surrounding the cells and blurry cell-cell boundaries when they are touching. The goal of this project was to develop image processing algorithms to analyze PCM images in an automated fashion, capable of processing large datasets of images to extract information related to cellular viability and morphology. To develop these algorithms, a large dataset of myoblasts images acquired in live-cell imaging (in PCM) was created, growing the cells in either a serum-supplemented (SSM) or a serum-free (SFM) medium over several passages. As a result, algorithms capable of computing the cell-covered surface and cellular morphological features were programmed in Matlab®. The cell-covered surface was estimated using a range filter, a threshold and a minimum cut size in order to look at the cellular growth kinetics. Results showed that the cells were growing at similar paces for both media, but their growth rate was decreasing linearly with passage number. The undecimated wavelet transform multivariate image analysis (UWT-MIA) method was developed, and was used to estimate cellular morphological features distributions (major axis, minor axis, orientation and roundness distributions) on a very large PCM image dataset using the Gabor continuous wavelet transform. Multivariate data analysis performed on the whole database (around 1 million PCM images) showed in a quantitative manner that myoblasts grown in SFM were more elongated and smaller than cells grown in SSM. The algorithms developed through this project could be used in the future on other cellular phenotypes for high-throughput screening and cell culture control applications