Signal denoising and viral particle identification in wide-field photon scattering parametric images using deep learning

Polarization parametric indirect microscopic imaging (PIMI) can obtain anisotropic nanoscale structural information of the sample by utilizing a polarization modulated illumination scheme and fitting the far-field variation of polarization states of the scattered photons. The rich scattering information of PIMI images can be exploited for identification of viral particles, aiming for early infection screening of viruses. Accurate processing and analysis of PIMI results is an important part of obtaining structural feature information of virus. Under noisy conditions, however, manually identifying viral particles in PIMI images is a very time-consuming process with a high error rate. The systematic noise degrading the image resolution and contrast are mainly due to the mechanical or electrical disturbance from the modulation of the illumination when taking raw images. To achieve efficient noise suppressing and accurate virus identification in PIMI images, we developed a neural network-based framework of algorithms. Firstly, a fairly effective denoising method particularly for PIMI imaging was proposed based on a generative network. Both the numerical and experimental results show that the developed method has the best capability of noise removal for PIMI images compared with the traditional denoising algorithms. Secondly, we use a convolutional neural network to detect and recognize viral particles in PIMI images. The experimental results show that viral particles can be identified in PIMI images with high accuracy

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

Domain-Aware Few-Shot Learning for Optical Coherence Tomography Noise Reduction

Speckle noise has long been an extensively studied problem in medical imaging. In recent years, there have been significant advances in leveraging deep learning methods for noise reduction. Nevertheless, adaptation of supervised learning models to unseen domains remains a challenging problem. Specifically, deep neural networks (DNNs) trained for computational imaging tasks are vulnerable to changes in the acquisition system's physical parameters, such as: sampling space, resolution, and contrast. Even within the same acquisition system, performance degrades across datasets of different biological tissues. In this work, we propose a few-shot supervised learning framework for optical coherence tomography (OCT) noise reduction, that offers a dramatic increase in training speed and requires only a single image, or part of an image, and a corresponding speckle suppressed ground truth, for training. Furthermore, we formulate the domain shift problem for OCT diverse imaging systems, and prove that the output resolution of a despeckling trained model is determined by the source domain resolution. We also provide possible remedies. We propose different practical implementations of our approach, verify and compare their applicability, robustness, and computational efficiency. Our results demonstrate significant potential for generally improving sample complexity, generalization, and time efficiency, for coherent and non-coherent noise reduction via supervised learning models, that can also be leveraged for other real-time computer vision applications

InSAR Deformation Analysis with Distributed Scatterers: A Review Complemented by New Advances

Interferometric Synthetic Aperture Radar (InSAR) is a powerful remote sensing technique able to measure deformation of the earth’s surface over large areas. InSAR deformation analysis uses two main categories of backscatter: Persistent Scatterers (PS) and Distributed Scatterers (DS). While PS are characterized by a high signal-to-noise ratio and predominantly occur as single pixels, DS possess a medium or low signal-to-noise ratio and can only be exploited if they form homogeneous groups of pixels that are large enough to allow for statistical analysis. Although DS have been used by InSAR since its beginnings for different purposes, new methods developed during the last decade have advanced the field significantly. Preprocessing of DS with spatio-temporal filtering allows today the use of DS in PS algorithms as if they were PS, thereby enlarging spatial coverage and stabilizing algorithms. This review explores the relations between different lines of research and discusses open questions regarding DS preprocessing for deformation analysis. The review is complemented with an experiment that demonstrates that significantly improved results can be achieved for preprocessed DS during parameter estimation if their statistical properties are used

Image analytic tools for tissue characterization using optical coherence tomography

Optical coherence tomography (OCT) has been emerging as a promising imaging technique, with a strong capability of non-invasive, in vivo, high resolution, depth-resolved imaging. There is a great potential to use OCT to guide the treatment of arrhythmias, to prevent preterm birth, and to detect breast cancer. To facilitate the clinical applications, this thesis presents three image analytic tools to characterize biological tissue: 1) automated fiber direction analysis; 2) automated volumetric stitching; 3) automated tissue classification. The fiber direction analysis consists of a particle-filter-based 3D tractography scheme and a pixel-wise fiber analysis scheme. The stitching algorithm enlarges the field of view of current OCT system from millimeter to centimeter level by volumetric stitching using scale-invariant feature transform. Based on relevance vector machine, a region-based classification scheme and a grid-based classification scheme are developed to automatically identify tissue composition in human cardiac tissue and human breast tissue. These tools are collaboratively used to study OCT images from cardiac, cervical, and breast tissue. In cardiac tissue, we apply the fiber orientation analysis to reconstruct 3D cardiac myofibers tractography and perform pixel-wise fiber analysis on the collagen region within human heart. In addition, we apply the region-based algorithm to segment and classify tissue compositions, such as collagen, adipose tissue, fibrotic myocardium, and normal myocardium, over a single or a stitched OCT volume. Using our algorithm, we observe fiber directionality change over depths and find that the fiber orientation changes more dramatically in atria than in ventricle. We also observe different dispersion patterns within collagen layer. In cervical tissue, our stitching algorithm enables a paramount 3D view of entire axial slices. Together with pixel-wise fiber orientation scheme, we analyze the difference of dispersion property within inner/outer regions of four quadrants. We observe two dispersion patterns in pregnant and non-pregnant cervical tissue at the location close to upper cervix. In addition, we discover that an increasing trend of dispersion and an increasing trend of penetration depth from internal orifice (os) to external os. In breast tissue, we visualize various features in both benign and malignant tissues such as invasive ductal carcinoma (IDC), ductal carcinoma in situ, cyst, and terminal duct lobule unit in stitched OCT images. Focusing on the automated detection of IDC, we propose a hierarchy framework of classification model and apply our classifier in two OCT systems and achieve both reasonable sensitivity and specificity in identifying cancerous region

Synthetic Aperture Radar (SAR) Meets Deep Learning

This reprint focuses on the application of the combination of synthetic aperture radars and depth learning technology. It aims to further promote the development of SAR image intelligent interpretation technology. A synthetic aperture radar (SAR) is an important active microwave imaging sensor, whose all-day and all-weather working capacity give it an important place in the remote sensing community. Since the United States launched the first SAR satellite, SAR has received much attention in the remote sensing community, e.g., in geological exploration, topographic mapping, disaster forecast, and traffic monitoring. It is valuable and meaningful, therefore, to study SAR-based remote sensing applications. In recent years, deep learning represented by convolution neural networks has promoted significant progress in the computer vision community, e.g., in face recognition, the driverless field and Internet of things (IoT). Deep learning can enable computational models with multiple processing layers to learn data representations with multiple-level abstractions. This can greatly improve the performance of various applications. This reprint provides a platform for researchers to handle the above significant challenges and present their innovative and cutting-edge research results when applying deep learning to SAR in various manuscript types, e.g., articles, letters, reviews and technical reports

Extraction d'informations de changement à partir des séries temporelles d'images radar à synthèse d'ouverture

A large number of successfully launched and operated Synthetic Aperture Radar (SAR) satellites has regularly provided multitemporal SAR and polarimetric SAR (PolSAR) images with high and very high spatial resolution over immense areas of the Earth surface. SAR system is appropriate for monitoring tasks thanks to the advantage of operating in all-time and all-weather conditions. With multitemporal data, both spatial and temporal information can simultaneously be exploited to improve the results of researche works. Change detection of specific features within a certain time interval has to deal with a complex processing of SAR data and the so-called speckle which affects the backscattered signal as multiplicative noise.The aim of this thesis is to provide a methodology for simplifying the analysis of multitemporal SAR data. Such methodology can benefit from the advantages of repetitive SAR acquisitions and be able to process different kinds of SAR data (i.e. single, multipolarization SAR, etc.) for various applications. In this thesis, we first propose a general framework based on a spatio-temporal information matrix called emph{Change Detection Matrix} (CDM). This matrix contains temporal neighborhoods which are adaptive to changed and unchanged areas thanks to similarity cross tests. Then, the proposed method is used to perform three different tasks:1) multitemporal change detection with different kinds of changes, which allows the combination of multitemporal pair-wise change maps to improve the performance of change detection result;2) analysis of change dynamics in the observed area, which allows the investigation of temporal evolution of objects of interest;3) nonlocal temporal mean filtering of SAR/PolSAR image time series, which allows us to avoid smoothing change information in the time series during the filtering process.In order to illustrate the relevancy of the proposed method, the experimental works of the thesis is performed on four datasets over two test-sites: Chamonix Mont-Blanc, France and Merapi volcano, Indonesia, with different types of changes (i.e., seasonal evolution, glaciers, volcanic eruption, etc.). Observations of these test-sites are performed on four SAR images time series from single polarization to full polarization, from medium to high, very high spatial resolution: Sentinel-1, ALOS-PALSAR, RADARSAT-2 and TerraSAR-X time series.La réussite du lancement d'un grand nombre des satellites Radar à Synthèse d'Ouverture (RSO - SAR) de nouvelle génération a fourni régulièrement des images SAR et SAR polarimétrique (PolSAR) multitemporelles à haute et très haute résolution spatiale sur de larges régions de la surface de la Terre. Le système SAR est approprié pour des tâches de surveillance continue ou il offre l'avantage d'être indépendant de l'éclairement solaire et de la couverture nuageuse. Avec des données multitemporelles, l'information spatiale et temporelle peut être exploitée simultanément pour rendre plus concise, l'extraction d'information à partir des données. La détection de changement de structures spécifiques dans un certain intervalle de temps nécessite un traitement complexe des données SAR et la présence du chatoiement (speckle) qui affecte la rétrodiffusion comme un bruit multiplicatif. Le but de cette thèse est de fournir une méthodologie pour simplifier l'analyse des données multitemporelles SAR. Cette méthodologie doit bénéficier des avantages d'acquisitions SAR répétitives et être capable de traiter différents types de données SAR (images SAR mono-, multi- composantes, etc.) pour diverses applications. Au cours de cette thèse, nous proposons tout d'abord une méthode générale basée sur une matrice d'information spatio-temporelle appelée Matrice de détection de changement (CDM). Cette matrice contient des informations de changements obtenus à partir de tests croisés de similarité sur des voisinages adaptatifs. La méthode proposée est ensuite exploitée pour réaliser trois tâches différentes: 1) la détection de changement multitemporel avec différents types de changements, ce qui permet la combinaison des cartes de changement entre des paires d'images pour améliorer la performance de résultat de détection de changement; 2) l'analyse de la dynamicité de changement de la zone observée, ce qui permet l'étude de l'évolution temporelle des objets d'intérêt; 3) le filtrage nonlocal temporel des séries temporelles d'images SAR/PolSAR, ce qui permet d'éviter le lissage des informations de changement dans des séries pendant le processus de filtrage.Afin d'illustrer la pertinence de la méthode proposée, la partie expérimentale de la thèse est effectuée sur deux sites d'étude: Chamonix Mont-Blanc, France et le volcan Merapi, Indonésie, avec différents types de changements (i.e. évolution saisonnière, glaciers, éruption volcanique, etc.). Les observations de ces sites d'étude sont acquises sur quatre séries temporelles d'images SAR monocomposantes et multicomposantes de moyenne à haute et très haute résolution: des séries temporelles d'images Sentinel-1, ALOS-PALSAR, RADARSAT-2 et TerraSAR-X