Impact of model parameters on Monte Carlo simulations of backscattering Mueller matrix images of colon tissue

Polarimetric imaging is emerging as a viable technique for tumor detection and staging. As a preliminary step towards a thorough understanding of the observed contrasts, we present a set of numerical Monte Carlo simulations of the polarimetric response of multilayer structures representing colon samples in the backscattering geometry. In a first instance, a typical colon sample was modeled as one or two scattering “slabs” with monodisperse non absorbing scatterers representing the most superficial tissue layers (the mucosa and submucosa), above a totally depolarizing Lambertian lumping the contributions of the deeper layers (muscularis and pericolic tissue). The model parameters were the number of layers, their thicknesses and morphology, the sizes and concentrations of the scatterers, the optical index contrast between the scatterers and the surrounding medium, and the Lambertian albedo. With quite similar results for single and double layer structures, this model does not reproduce the experimentally observed stability of the relative magnitudes of the depolarizing powers for incident linear and circular polarizations. This issue was solved by considering bimodal populations including large and small scatterers in a single layer above the Lambertian, a result which shows the importance of taking into account the various types of scatterers (nuclei, collagen fibers and organelles) in the same model

Development of polarization-resolved optical scanning microscopy imaging techniques to study biomolecular organizations

Light, as electromagnetic radiation, conveys energy through space and time via fluctuations in electric and magnetic fields. This thesis explores the interaction of light and biological structures through polarization-resolved imaging techniques. Light microscopy, and polarization analysis enable the examination of biological entities. Biological function often centers on chromatin, the genetic material composed of DNA wrapped around histone proteins within cell nuclei. This structure's chiral nature gives rise to interactions with polarized light. This research encompasses three main aspects. Firstly, an existing multimodal Circular Intensity Differential Scattering (CIDS) and fluorescence microscopy are upgraded into an open configuration to be integrated with other modalities. Secondly, a novel cell classification method employing CIDS and a phasor representation is introduced. Thirdly, polarization analysis of fluorescence emission is employed for pathological investigations. Accordingly, the thesis is organized into three chapters. Chapter 1 lays the theoretical foundation for light propagation and polarization, outlining the Jones and Stokes-Mueller formalisms. The interaction between light and optical elements, transmission, and reflection processes are discussed. Polarized light's ability to reveal image contrast in polarizing microscopes, linear and nonlinear polarization-resolved microscopy, and Mueller matrix microscopy as a comprehensive technique for studying biological structures are detailed. Chapter 2 focuses on CIDS, a label-free light scattering method, including a single point angular spectroscopy mode and scanning microscopy imaging. A significant upgrade of the setup is achieved, incorporating automation, calibration, and statistical analysis routines. An intuitive phasor approach is proposed, enabling image segmentation, cell discrimination, and enhanced interpretation of polarimetric contrast. As a result, image processing programs have been developed to provide automated measurements using polarization-resolved laser scanning microscopy imaging integrated with confocal fluorescence microscopy of cells and chromatin inside cell nuclei, including the use of new types of samples such as progeria cells. Chapter 3 applies a polarization-resolved two-photon excitation fluorescence (2PEF) microscopy to study multicellular cancerous cells. A homemade 2PEF microscope is developed for colon cancer cell analysis. The integration of polarization and fluorescence techniques leads to a comprehensive understanding of the molecular orientation within samples, particularly useful for cancer diagnosis. Overall, this thesis presents an exploration of polarization-resolved imaging techniques for studying biological structures, encompassing theory, experimental enhancements, innovative methodologies, and practical applications

Kinetics of optical properties of human colorectal tissues during optical clearing: a comparative study between normal and pathological tissues

To characterize the optical clearing treatments in human colorectal tissues and possibly to differentiate between treatments of normal and pathological tissues, we have used a simple indirect method derived from Mie scattering theory to estimate the kinetics of the reduced scattering coefficient. A complementary method to estimate the kinetics of the scattering coefficient is also used so that the kinetics of the anisotropy factor and of the refractive index are also calculated. Both methods rely only on the thickness and collimated transmittance measurements made during treatment. The results indicate the expected time dependencies for the optical properties of both tissues: an increase in the refractive index and anisotropy factor and a decrease in the scattering coefficients. The similarity in the kinetics obtained for normal and pathological tissues indicates that optical clearing treatments can be applied also in pathological tissues to produce similar effects. The estimated time dependencies using experimental spectral data in the range from 400 to 1000 nm allowed us to compare the kinetics of the optical properties between different wavelengths.info:eu-repo/semantics/publishedVersio

Monitoring wetlands and water bodies in semi-arid Sub-Saharan regions

Surface water in wetlands is a critical resource in semi-arid West-African regions that are frequently exposed to droughts. Wetlands are of utmost importance for the population as well as the environment, and are subject to rapidly changing seasonal fluctuations. Dynamics of wetlands in the study area are still poorly understood, and the potential of remote sensing-derived information as a large-scale, multi-temporal, comparable and independent measurement source is not exploited. This work shows successful wetland monitoring with remote sensing in savannah and Sahel regions in Burkina Faso, focusing on the main study site Lac Bam (Lake Bam). Long-term optical time series from MODIS with medium spatial resolution (MR), and short-term synthetic aperture radar (SAR) time series from TerraSAR-X and RADARSAT-2 with high spatial resolution (HR) successfully demonstrate the classification and dynamic monitoring of relevant wetland features, e.g. open water, flooded vegetation and irrigated cultivation. Methodological highlights are time series analysis, e.g. spatio-temporal dynamics or multitemporal-classification, as well as polarimetric SAR (polSAR) processing, i.e. the Kennaugh elements, enabling physical interpretation of SAR scattering mechanisms for dual-polarized data. A multi-sensor and multi-frequency SAR data combination provides added value, and reveals that dual-co-pol SAR data is most recommended for monitoring wetlands of this type. The interpretation of environmental or man-made processes such as water areas spreading out further but retreating or evaporating faster, co-occurrence of droughts with surface water and vegetation anomalies, expansion of irrigated agriculture or new dam building, can be detected with MR optical and HR SAR time series. To capture long-term impacts of water extraction, sedimentation and climate change on wetlands, remote sensing solutions are available, and would have great potential to contribute to water management in Africa

Optical Diagnostics in Human Diseases

Optical technologies provide unique opportunities for the diagnosis of various pathological disorders. The range of biophotonics applications in clinical practice is considerably wide given that the optical properties of biological tissues are subject to significant changes during disease progression. Due to the small size of studied objects (from μm to mm) and despite some minimum restrictions (low-intensity light is used), these technologies have great diagnostic potential both as an additional tool and in cases of separate use, for example, to assess conditions affecting microcirculatory bed and tissue viability. This Special Issue presents topical articles by researchers engaged in the development of new methods and devices for optical non-invasive diagnostics in various fields of medicine. Several studies in this Special Issue demonstrate new information relevant to surgical procedures, especially in oncology and gynecology. Two articles are dedicated to the topical problem of breast cancer early detection, including during surgery. One of the articles is devoted to urology, namely to the problem of chronic or recurrent episodic urethral pain. Several works describe the studies in otolaryngology and dentistry. One of the studies is devoted to diagnosing liver diseases. A number of articles contribute to the studying of the alterations caused by diabetes mellitus and cardiovascular diseases. The results of all the presented articles reflect novel innovative research and emerging ideas in optical non-invasive diagnostics aimed at their wider translation into clinical practice

Advanced Geoscience Remote Sensing

Nowadays, advanced remote sensing technology plays tremendous roles to build a quantitative and comprehensive understanding of how the Earth system operates. The advanced remote sensing technology is also used widely to monitor and survey the natural disasters and man-made pollution. Besides, telecommunication is considered as precise advanced remote sensing technology tool. Indeed precise usages of remote sensing and telecommunication without a comprehensive understanding of mathematics and physics. This book has three parts (i) microwave remote sensing applications, (ii) nuclear, geophysics and telecommunication; and (iii) environment remote sensing investigations

Combining omnidirectional vision with polarization vision for robot navigation

La polarisation est le phénomène qui décrit les orientations des oscillations des ondes lumineuses qui sont limitées en direction. La lumière polarisée est largement utilisée dans le règne animal,à partir de la recherche de nourriture, la défense et la communication et la navigation. Le chapitre (1) aborde brièvement certains aspects importants de la polarisation et explique notre problématique de recherche. Nous visons à utiliser un capteur polarimétrique-catadioptrique car il existe de nombreuses applications qui peuvent bénéficier d'une telle combinaison en vision par ordinateur et en robotique, en particulier pour l'estimation d'attitude et les applications de navigation. Le chapitre (2) couvre essentiellement l'état de l'art de l'estimation d'attitude basée sur la vision.Quand la lumière non-polarisée du soleil pénètre dans l'atmosphère, l'air entraine une diffusion de Rayleigh, et la lumière devient partiellement linéairement polarisée. Le chapitre (3) présente les motifs de polarisation de la lumière naturelle et couvre l'état de l'art des méthodes d'acquisition des motifs de polarisation de la lumière naturelle utilisant des capteurs omnidirectionnels (par exemple fisheye et capteurs catadioptriques). Nous expliquons également les caractéristiques de polarisation de la lumière naturelle et donnons une nouvelle dérivation théorique de son angle de polarisation.Notre objectif est d'obtenir une vue omnidirectionnelle à 360 associée aux caractéristiques de polarisation. Pour ce faire, ce travail est basé sur des capteurs catadioptriques qui sont composées de surfaces réfléchissantes et de lentilles. Généralement, la surface réfléchissante est métallique et donc l'état de polarisation de la lumière incidente, qui est le plus souvent partiellement linéairement polarisée, est modifiée pour être polarisée elliptiquement après réflexion. A partir de la mesure de l'état de polarisation de la lumière réfléchie, nous voulons obtenir l'état de polarisation incident. Le chapitre (4) propose une nouvelle méthode pour mesurer les paramètres de polarisation de la lumière en utilisant un capteur catadioptrique. La possibilité de mesurer le vecteur de Stokes du rayon incident est démontré à partir de trois composants du vecteur de Stokes du rayon réfléchi sur les quatre existants.Lorsque les motifs de polarisation incidents sont disponibles, les angles zénithal et azimutal du soleil peuvent être directement estimés à l'aide de ces modèles. Le chapitre (5) traite de l'orientation et de la navigation de robot basées sur la polarisation et différents algorithmes sont proposés pour estimer ces angles dans ce chapitre. A notre connaissance, l'angle zénithal du soleil est pour la première fois estimé dans ce travail à partir des schémas de polarisation incidents. Nous proposons également d'estimer l'orientation d'un véhicule à partir de ces motifs de polarisation.Enfin, le travail est conclu et les possibles perspectives de recherche sont discutées dans le chapitre (6). D'autres exemples de schémas de polarisation de la lumière naturelle, leur calibrage et des applications sont proposées en annexe (B).Notre travail pourrait ouvrir un accès au monde de la vision polarimétrique omnidirectionnelle en plus des approches conventionnelles. Cela inclut l'orientation bio-inspirée des robots, des applications de navigation, ou bien la localisation en plein air pour laquelle les motifs de polarisation de la lumière naturelle associés à l'orientation du soleil à une heure précise peuvent aboutir à la localisation géographique d'un véhiculePolarization is the phenomenon that describes the oscillations orientations of the light waves which are restricted in direction. Polarized light has multiple uses in the animal kingdom ranging from foraging, defense and communication to orientation and navigation. Chapter (1) briefly covers some important aspects of polarization and explains our research problem. We are aiming to use a polarimetric-catadioptric sensor since there are many applications which can benefit from such combination in computer vision and robotics specially robot orientation (attitude estimation) and navigation applications. Chapter (2) mainly covers the state of art of visual based attitude estimation.As the unpolarized sunlight enters the Earth s atmosphere, it is Rayleigh-scattered by air, and it becomes partially linearly polarized. This skylight polarization provides a signi cant clue to understanding the environment. Its state conveys the information for obtaining the sun orientation. Robot navigation, sensor planning, and many other applications may bene t from using this navigation clue. Chapter (3) covers the state of art in capturing the skylight polarization patterns using omnidirectional sensors (e.g fisheye and catadioptric sensors). It also explains the skylight polarization characteristics and gives a new theoretical derivation of the skylight angle of polarization pattern. Our aim is to obtain an omnidirectional 360 view combined with polarization characteristics. Hence, this work is based on catadioptric sensors which are composed of reflective surfaces and lenses. Usually the reflective surface is metallic and hence the incident skylight polarization state, which is mostly partially linearly polarized, is changed to be elliptically polarized after reflection. Given the measured reflected polarization state, we want to obtain the incident polarization state. Chapter (4) proposes a method to measure the light polarization parameters using a catadioptric sensor. The possibility to measure the incident Stokes is proved given three Stokes out of the four reflected Stokes. Once the incident polarization patterns are available, the solar angles can be directly estimated using these patterns. Chapter (5) discusses polarization based robot orientation and navigation and proposes new algorithms to estimate these solar angles where, to the best of our knowledge, the sun zenith angle is firstly estimated in this work given these incident polarization patterns. We also propose to estimate any vehicle orientation given these polarization patterns. Finally the work is concluded and possible future research directions are discussed in chapter (6). More examples of skylight polarization patterns, their calibration, and the proposed applications are given in appendix (B). Our work may pave the way to move from the conventional polarization vision world to the omnidirectional one. It enables bio-inspired robot orientation and navigation applications and possible outdoor localization based on the skylight polarization patterns where given the solar angles at a certain date and instant of time may infer the current vehicle geographical location.DIJON-BU Doc.électronique (212319901) / SudocSudocFranceF

Avian Attractiveness to Vertically Polarized Light

It is well-known that many animal species can detect polarized light cues of water and water-like objects in the visible and ultraviolet range. However, studies investigating if birds can see polarized light in field-based settings are rare. Furthermore, no studies have yet been conducted to understand avian attractiveness to vertically polarized light, nor have studies considered other natural polarizers of light such as tree sap. I designed a choice-field experiment to investigate if birds can detect, and are attracted to vertically polarized light. First, I cut six pieces of clear vinyl into a foot by 54 inches. I painted each vinyl sheet with Black 3.0, advertised as the blackest paint in the world. Two treatments were wrapped around two trees similar in dbh (\u3c40 dbh) and close in distance (\u3c5 feet): one had shiny exposed, and the other matte, painted side, exposed. Suet feeders were hung directly below each treatment on both trees. Two remote cameras were placed on a fence post away from both tree (10 feet in fall; 6 feet in spring). The suet feeder height, camera distance, and the height of both vinyl stayed the same. These treatments were exposed to birds. A baseline study was conducted before installation of treatments to understand bird biases or preferences to one tree position over the other. I made conclusions about birds being able to see, and their attraction to, vertically polarized light by capturing and counting visitations from images, and comparing treatments’ bird visits over a designated period of time. My results revealed that birds are able to detect and are attracted to vertically polarized light, and use it to guide foraging behavior. Attraction to polarized light is dependent upon the location of the site, as well as the position (left or right tree), and certain species may play a role in these conclusions, though they do not overwhelm the data. The baseline study to treatment comparison reveals that any preferences to one position over the other were eliminated when treatments were added, and the polarized, shiny treatment had more of a signal than the matte treatment when each treatment were compared separately to the baseline. These results suggest a need to expand site-wise across various habitats to understand the effects of site location, to understand the effects of the positionality of treatments on different species of trees, and to understand how different species may have an effect on treatment visitation. Sap was imaged using a polarimeter to understand if natural Maple sap polarizes light compared to my polarized proxy for sap. My analyses reveal that natural Maple sap polarizes light, and this is strongest in the ultraviolet range. My treatments polarize a high degree of light in both the visible and ultraviolet range, making it an effective simulator of natural Maple sap. This exciting discovery gives insight on how birds may navigate a complex landscape according to polarized cues of that landscape (polarization of sap), and how they use these cues to facilitate their foraging behavior (eating sap)