Snapshot multispectral oximetry using image replication and birefringent spectrometry

This thesis describes the improvements to the image replicating imaging spectrometer (IRIS) and the development of novel applications in the field of oximetry. IRIS is a snapshot multispectral device with a high transmission output and no need of inversion for data recovering, hence, with high signal-to-noise ratio (SNR). IRIS shows great versatility due to the possibility of choosing multiple contiguous or non-contiguous wavelengths inside its free spectral range. IRIS uses a set of waveplates and Wollaston prisms to demultiplex the spectral information of an object and replicate the image of such object in different wavelengths. The birefringent nature of IRIS means that different wavelengths are separated by the Wollaston prisms with different angles, introducing multiple images of the same object. In addition, the spectral transmission function shows multiple spectral sidelobes that contaminate each IRIS band with light belonging to other wavelengths. These issues can lower the performance of IRIS as a multispectral imaging device. In this thesis, these problems were assessed with the introduction of a filter plate array placed in the image plane of the optical system. This filter array is a set of narrow-band filters (Full Width Half Maximum (FWHM) =10 ± 2 nm ) that removes undesired wavelengths from each IRIS band. Since the spectral transmission of IRIS is replicated along the free spectral range, the filters can be designed to match any of the present spectral lobes in IRIS. The design and fabrication of a filter array enhance the performance of IRIS as a multispectral imaging device: it allows wavelength selection and improves spectral and spatial image quality. The design and manufacture of the corresponding filter holder and camera adapter were critical in terms of offering an easy filter-camera implementation. The filter plate allowed the removal of other dispersed wavelengths by the Wollaston prisms, improving image registration between the set of spectral images created by IRIS, and so, improving the quality of the registered spectral 3-D cube. The implemented improvements on IRIS allow high quality, calibration-free oximetry using eight different wavelengths optimised for oximetry. Two main experiments were performed: 1) Using an inverted microscopy interfaced with IRIS and a linear spectral unmixing technique, we measured the deoxygenation of single horse red blood cells (RBC) in vitro in real time. The oximetry was performed with a subcellular spatial resolution of 0.5 μ m , a temporal resolution of 30 Hz, and an accuracy (standard error of the mean) of ± 1.1% in oxygen saturation. 2) Eight-wavelength calibration-free retinal oximetry performed in nine healthy subjects demonstrated an increase in the stability of the oxygen saturation measurements along retinal vessels when compared with more traditional analysis methods such as two wavelengths oximetry. The stability was measured as the standard deviation along the retinal vessels of the nine subjects and was found to be ∼ 3% in oxygen saturation for eight-wavelengths oximetry and ∼ 5% in oxygen saturation for two-wavelengths oximetry. A modified physical model was used to improve the characterization of light propagation through the eye, retina, and blood vessels by applying a set of feasible physiological assumptions. This model was optimised by an algorithm which solves for the different variables involved in the retinal vessels transmissions in order to accurately calculate the oxygen saturation. The oximetry algorithm was applied in retinal vessels, in collaboration in vivo on rat spinal cord to assess hypoxia in inflammatory diseases such as multiple sclerosis and rheumatoid arthritis and on mice legs to assess hypoxia on autoimmune diseases. A third experiment using a microscope interfaced with IRIS was performed. The experiment aimed to replicate laminar flow conditions observed in retinal vessels and to calculate oxygen diffusion between adjacent streams of blood with different oxygen saturation. For this purpose a PDMS multichannel flow cell with cross sections of 40x100 μm was designed and fabricated allowing us to replicate conditions found in retinal blood vessels. Laminar flow was replicated but the experiment failed in calculating oxygen diffusion due to flaws in the experiment. The experiment with the results and recommendations on how to improve it can be found in Apendix B for future researcher

Image Restoration

This book represents a sample of recent contributions of researchers all around the world in the field of image restoration. The book consists of 15 chapters organized in three main sections (Theory, Applications, Interdisciplinarity). Topics cover some different aspects of the theory of image restoration, but this book is also an occasion to highlight some new topics of research related to the emergence of some original imaging devices. From this arise some real challenging problems related to image reconstruction/restoration that open the way to some new fundamental scientific questions closely related with the world we interact with

Modeling and applications of the focus cue in conventional digital cameras

El enfoque en cámaras digitales juega un papel fundamental tanto en la calidad de la imagen como en la percepción del entorno. Esta tesis estudia el enfoque en cámaras digitales convencionales, tales como cámaras de móviles, fotográficas, webcams y similares. Una revisión rigurosa de los conceptos teóricos detras del enfoque en cámaras convencionales muestra que, a pasar de su utilidad, el modelo clásico del thin lens presenta muchas limitaciones para aplicación en diferentes problemas relacionados con el foco. En esta tesis, el focus profile es propuesto como una alternativa a conceptos clásicos como la profundidad de campo. Los nuevos conceptos introducidos en esta tesis son aplicados a diferentes problemas relacionados con el foco, tales como la adquisición eficiente de imágenes, estimación de profundidad, integración de elementos perceptuales y fusión de imágenes. Los resultados experimentales muestran la aplicación exitosa de los modelos propuestos.The focus of digital cameras plays a fundamental role in both the quality of the acquired images and the perception of the imaged scene. This thesis studies the focus cue in conventional cameras with focus control, such as cellphone cameras, photography cameras, webcams and the like. A deep review of the theoretical concepts behind focus in conventional cameras reveals that, despite its usefulness, the widely known thin lens model has several limitations for solving different focus-related problems in computer vision. In order to overcome these limitations, the focus profile model is introduced as an alternative to classic concepts, such as the near and far limits of the depth-of-field. The new concepts introduced in this dissertation are exploited for solving diverse focus-related problems, such as efficient image capture, depth estimation, visual cue integration and image fusion. The results obtained through an exhaustive experimental validation demonstrate the applicability of the proposed models

Coronagraph particulate measurements. Skylab flight experiment T025

Major results of the Skylab T025 Coronagraph experiment designed to monitor the particulate contamination about the spacecraft and to study the earth's atmospheric aerosol distribution are presented. A model for comet outbursts based on the properties of amorphous ice and ground based narrow-band and white light photography of comet Kohoutek ten days to perihelion are included. The effect of atmospheric refraction on the analysis of the T025 atmospheric data was also investigated

Colour depth-from-defocus incorporating experimental point spread function measurements

Depth-From-Defocus (DFD) is a monocular computer vision technique for creating depth maps from two images taken on the same optical axis with different intrinsic camera parameters. A pre-processing stage for optimally converting colour images to monochrome using a linear combination of the colour planes has been shown to improve the accuracy of the depth map. It was found that the first component formed using Principal Component Analysis (PCA) and a technique to maximise the signal-to-noise ratio (SNR) performed better than using an equal weighting of the colour planes with an additive noise model. When the noise is non-isotropic the Mean Square Error (MSE) of the depth map by maximising the SNR was improved by 7.8 times compared to an equal weighting and 1.9 compared to PCA. The fractal dimension (FD) of a monochrome image gives a measure of its roughness and an algorithm was devised to maximise its FD through colour mixing. The formulation using a fractional Brownian motion (mm) model reduced the SNR and thus produced depth maps that were less accurate than using PCA or an equal weighting. An active DFD algorithm to reduce the image overlap problem has been developed, called Localisation through Colour Mixing (LCM), that uses a projected colour pattern. Simulation results showed that LCM produces a MSE 9.4 times lower than equal weighting and 2.2 times lower than PCA. The Point Spread Function (PSF) of a camera system models how a point source of light is imaged. For depth maps to be accurately created using DFD a high-precision PSF must be known. Improvements to a sub-sampled, knife-edge based technique are presented that account for non-uniform illumination of the light box and this reduced the MSE by 25%. The Generalised Gaussian is presented as a model of the PSF and shown to be up to 16 times better than the conventional models of the Gaussian and pillbox

Transillumination techniques in ophthalmic imaging

In vivo imaging of the human cornea and retina is typically performed in a reflection geometry. Images are formed from light that has backscattered off corneal microstructures or backreflected from the retina. In this configuration, artifacts caused by superficial surface reflections are often encountered. These unwanted reflections can either globally overwhelm the signal or cause local glare, complicating reliable image quantification. This thesis describes a pair of alternative ophthalmic imaging techniques based instead on transmitted light, which inherently avoids these artifacts. For retinal (i.e. fundus) imaging, we describe a mesoscopic transmission imaging method, which we call transcranial fundus imaging. The method uses deeply penetrating near-infrared light delivered transcranially from the side of the head, and exploits multiple scattering to redirect a portion of the light towards the posterior eye. This unique transmission geometry simplifies absorption measurements and enables flash-free, non-mydriatic imaging as deep as the choroid. We use multispectral image sets taken with this new transillumination approach to estimate oxygen saturation in retinal blood vessels. In the cornea, we describe a new technique for non-contact phase-contrast microscopic imaging. It is based on fundus retro-reflection and back-illumination of the crystalline lens and cornea. To enhance phase-gradient contrast, we apply asymmetric illumination by illuminating one side of the fundus. The technique produces micron-scale lateral resolution across a 1-mm diagonal field of view. We show representative images of the epithelium, the subbasal nerve plexus, large stromal nerves, dendritic immune cells, endothelial nuclei, and the anterior crystalline lens, demonstrating the potential of this instrument for clinical applications

Quantitative Optical Imaging and Sensing by Joint Design of Point Spread Functions and Estimation Algorithms

The joint application of tailored optical Point Spread Functions (PSF) and estimation methods is an important tool for designing quantitative imaging and sensing solutions. By enhancing the information transfer encoded by the optical waves into an image, matched post-processing algorithms are able to complete tasks with improved performance relative to conventional designs. In this thesis, new engineered PSF solutions with image processing algorithms are introduced and demonstrated for quantitative imaging using information-efficient signal processing tools and/or optical-efficient experimental implementations. The use of a 3D engineered PSF, the Double-Helix (DH-PSF), is applied as one solution for three-dimensional, super-resolution fluorescence microscopy. The DH-PSF is a tailored PSF which was engineered to have enhanced information transfer for the task of localizing point sources in three dimensions. Both an information- and optical-efficient implementation of the DH-PSF microscope are demonstrated here for the first time. This microscope is applied to image single-molecules and micro-tubules located within a biological sample. A joint imaging/axial-ranging modality is demonstrated for application to quantifying sources of extended transverse and axial extent. The proposed implementation has improved optical-efficiency relative to prior designs due to the use of serialized cycling through select engineered PSFs. This system is demonstrated for passive-ranging, extended Depth-of-Field imaging and digital refocusing of random objects under broadband illumination. Although the serialized engineered PSF solution is an improvement over prior designs for the joint imaging/passive-ranging modality, it requires the use of multiple PSFs - a potentially significant constraint. Therefore an alternative design is proposed, the Single-Helix PSF, where only one engineered PSF is necessary and the chromatic behavior of objects under broadband illumination provides the necessary information transfer. The matched estimation algorithms are introduced along with an optically-efficient experimental system to image and passively estimate the distance to a test object. An engineered PSF solution is proposed for improving the sensitivity of optical wave-front sensing using a Shack-Hartmann Wave-front Sensor (SHWFS). The performance limits of the classical SHWFS design are evaluated and the engineered PSF system design is demonstrated to enhance performance. This system is fabricated and the mechanism for additional information transfer is identified

Anterior segment topography and aberrations for clinical applications

En esta tesis se ha llevado a cabo el desarrollo de un Tomógrafo de Coherencia Óptica (OCT) para visualizar en alta resolución y cuantificar tridimensionalmente el segmento anterior del ojo y se ha adaptado el aberrómetro Trazado de Rayos Laser (LRT) para medir las aberraciones oculares en distintas condiciones: queratocono y su tratamiento con anillos intracorneales (ICRS), estimulando la acomodación y en pacientes con lentes intraoculares (IOL). En particular, (1) se analiza la geometría de la córnea y las aberraciones en pacientes con queratocono antes y después de la cirugía de ICRS, y se analiza la posición de los ICRS; (2) se evalúa por primera vez in vivo la topografía del cristalino con la acomodación; (3) se analiza por primera vez la posición tridimensional y el impacto visual de las IOL acomodativas; y (4) se analiza in vivo la aberración cromática longitudinal en pacientes con IOL.Instituto Universitario de Oftalmobiología Aplicad

Robust density modelling using the student's t-distribution for human action recognition

The extraction of human features from videos is often inaccurate and prone to outliers. Such outliers can severely affect density modelling when the Gaussian distribution is used as the model since it is highly sensitive to outliers. The Gaussian distribution is also often used as base component of graphical models for recognising human actions in the videos (hidden Markov model and others) and the presence of outliers can significantly affect the recognition accuracy. In contrast, the Student's t-distribution is more robust to outliers and can be exploited to improve the recognition rate in the presence of abnormal data. In this paper, we present an HMM which uses mixtures of t-distributions as observation probabilities and show how experiments over two well-known datasets (Weizmann, MuHAVi) reported a remarkable improvement in classification accuracy. © 2011 IEEE

Endoscopic Laser Speckle Contrast Analysis for Tissue Perfusion

Laser speckle contrast analysis (LASCA), as a method of measuring blood flow speed and tissue perfusion, is a full field imaging technique requiring simple configurations and data processing, which is important for the application in real time in vivo. But LASCA is sensitive to changes in environmental factors. The application in vivo is also limited to superficial detection due to the limitation of the light penetration depth. Therefore this thesis aims to develop an endoscopic LASCA system to extend the access to internal detection and explore the relationship between the contrast and experimental parameters. Firstly the relationship between the contrast and speckle size, flow mode, quantity of stationary scatterers and the signal intensity were investigated. Theoretical models for the relationship between the contrast and the mean intensity of the speckle pattern were deduced and the correction methods were introduced to correct the contrast bias due to the intensity difference. Then a flexible single wavelength endoscopic laser speckle contrast analysis system (ELASCA) was developed using a leached fibre image guide (LFIG). A Butterworth filter and defocus were used to remove the fibre pattern to retrieve the contrast images. This system and the data processing methods were used on a customized phantom demonstrating that this ELASCA system can detect the flow speed changes in an imaging domain. Afterwards a dual-wavelength ELASCA was developed for functional imaging of the blood circulation. The test on a human fingertip and rabbit uterine blood vessels show that this system can monitor the change of blood flow speed and the oxygen saturation introduced by occlusion, in addition to the cardiac pulse and respiration rate. Then a novel application of LASCA to visualize the ultrasound pressure field and the propagation of the shear wave is presented for the application of locating area of interest (AOI) and detecting tissue variation