Virtual Microscopy with Extended Depth of Field

In this paper, we describe a virtual microscope system, based on JPEG 2000, which utilizes extended depth of field (EDF) imaging. Through a series of observer trials we show that EDF imaging improves both the local image quality of individual fields of view (FOV) and the accuracy with which the FOVs can be mosaiced (stitched) together. In addition, we estimate the required bit rate to adequately render a set of histology and cytology specimens at a quality suitable for on-line learning and collaboration. We show that, using JPEG 2000, we can efficiently represent high-quality, high-resolution colour images of microscopic specimens with less than 1 bit per pixel

Extended Field Laser Confocal Microscopy (EFLCM): Combining automated Gigapixel image capture with in silico virtual microscopy

<p>Abstract</p> <p>Background</p> <p>Confocal laser scanning microscopy has revolutionized cell biology. However, the technique has major limitations in speed and sensitivity due to the fact that a single laser beam scans the sample, allowing only a few microseconds signal collection for each pixel. This limitation has been overcome by the introduction of parallel beam illumination techniques in combination with cold CCD camera based image capture.</p> <p>Methods</p> <p>Using the combination of microlens enhanced Nipkow spinning disc confocal illumination together with fully automated image capture and large scale <it>in silico </it>image processing we have developed a system allowing the acquisition, presentation and analysis of maximum resolution confocal panorama images of several Gigapixel size. We call the method Extended Field Laser Confocal Microscopy (EFLCM).</p> <p>Results</p> <p>We show using the EFLCM technique that it is possible to create a continuous confocal multi-colour mosaic from thousands of individually captured images. EFLCM can digitize and analyze histological slides, sections of entire rodent organ and full size embryos. It can also record hundreds of thousands cultured cells at multiple wavelength in single event or time-lapse fashion on fixed slides, in live cell imaging chambers or microtiter plates.</p> <p>Conclusion</p> <p>The observer independent image capture of EFLCM allows quantitative measurements of fluorescence intensities and morphological parameters on a large number of cells. EFLCM therefore bridges the gap between the mainly illustrative fluorescence microscopy and purely quantitative flow cytometry. EFLCM can also be used as high content analysis (HCA) instrument for automated screening processes.</p

Coarse-grained Multiresolution Structures for Mobile Exploration of Gigantic Surface Models

We discuss our experience in creating scalable systems for distributing and rendering gigantic 3D surfaces on web environments and common handheld devices. Our methods are based on compressed streamable coarse-grained multiresolution structures. By combining CPU and GPU compression technology with our multiresolution data representation, we are able to incrementally transfer, locally store and render with unprecedented performance extremely detailed 3D mesh models on WebGL-enabled browsers, as well as on hardware-constrained mobile devices

Image Stitching

Projecte final de carrera fet en col.laboració amb University of Limerick. Department of Electronic and Computer EngineeringEnglish: Image processing is any form of signal processing for which the input is an image, such as a photograph or video frame; the output of image processing may be either an image or, a set of characteristics or parameters related to the image. Most image processing techniques involve treating the image as a two-dimensional signal and applying standard signal processing techniques to it. Specifically, image stitching presents different stages to render two or more overlapping images into a seamless stitched image, from the detection of features to blending in a final image. In this process, Scale Invariant Feature Transform (SIFT) algorithm can be applied to perform the detection and matching control points step, due to its good properties. The process of create an automatic and effective whole stitching process leads to analyze different methods of the stitching stages. Several commercial and online software tools are available to perform the stitching process, offering diverse options in different situations. This analysis involves the creation of a script to deal with images and project data files. Once the whole script is generated, the stitching process is able to achieve an automatic execution allowing good quality results in the final composite image.Castellano: Procesado de imagen es cualquier tipo de procesado de señal en aquel que la entrada es una imagen, como una fotografía o fotograma de video; la salida puede ser una imagen o conjunto de características y parámetros relacionados con la imagen. Muchas de las técnicas de procesado de imagen implican un tratamiento de la imagen como señal en dos dimensiones, y para ello se aplican técnicas estándar de procesado de señal. Concretamente, la costura o unión de imágenes presenta diferentes etapas para unir dos o más imágenes superpuestas en una imagen perfecta sin costuras, desde la detección de puntos clave en las imágenes hasta su mezcla en la imagen final. En este proceso, el algoritmo Scale Invariant Feature Transform (SIFT) puede ser aplicado para desarrollar la fase de detección y selección de correspondencias entre imágenes debido a sus buenas cualidades. El desarrollo de la creación de un completo proceso de costura automático y efectivo, pasa por analizar diferentes métodos de las etapas del cosido de las imágenes. Varios software comerciales y gratuitos son capaces de llevar a cabo el proceso de costura, ofreciendo diferentes alternativas en distintas situaciones. Este análisis implica la creación de una secuencia de comandos que trabaja con las imágenes y con archivos de datos del proyecto generado. Una vez esta secuencia es creada, el proceso de cosido de imágenes es capaz de lograr una ejecución automática permitiendo unos resultados de calidad en la imagen final.Català: Processament d'imatge és qualsevol tipus de processat de senyal en aquell que l'entrada és una imatge, com una fotografia o fotograma de vídeo, i la sortida pot ser una imatge o conjunt de característiques i paràmetres relacionats amb la imatge. Moltes de les tècniques de processat d'imatge impliquen un tractament de la imatge com a senyal en dues dimensions, i per això s'apliquen tècniques estàndard de processament de senyal. Concretament, la costura o unió d'imatges presenta diferents etapes per unir dues o més imatges superposades en una imatge perfecta sense costures, des de la detecció de punts clau en les imatges fins a la seva barreja en la imatge final. En aquest procés, l'algoritme Scale Invariant Feature Transform (SIFT) pot ser aplicat per desenvolupar la fase de detecció i selecció de correspondències entre imatges a causa de les seves bones qualitats. El desenvolupament de la creació d'un complet procés de costura automàtic i efectiu, passa per analitzar diferents mètodes de les etapes del cosit de les imatges. Diversos programari comercials i gratuïts són capaços de dur a terme el procés de costura, oferint diferents alternatives en diverses situacions. Aquesta anàlisi implica la creació d'una seqüència de commandes que treballa amb les imatges i amb arxius de dades del projecte generat. Un cop aquesta seqüència és creada, el procés de cosit d'imatges és capaç d'aconseguir una execució automàtica permetent uns resultats de qualitat en la imatge final

Remote Visual Observation of Real Places Through Virtual Reality Headsets

Virtual Reality has always represented a fascinating yet powerful opportunity that has attracted studies and technology developments, especially since the latest release on the market of powerful high-resolution and wide field-of-view VR headsets. While the great potential of such VR systems is common and accepted knowledge, issues remain related to how to design systems and setups capable of fully exploiting the latest hardware advances. The aim of the proposed research is to study and understand how to increase the perceived level of realism and sense of presence when remotely observing real places through VR headset displays. Hence, to produce a set of guidelines that give directions to system designers about how to optimize the display-camera setup to enhance performance, focusing on remote visual observation of real places. The outcome of this investigation represents unique knowledge that is believed to be very beneficial for better VR headset designs towards improved remote observation systems. To achieve the proposed goal, this thesis presents a thorough investigation of existing literature and previous researches, which is carried out systematically to identify the most important factors ruling realism, depth perception, comfort, and sense of presence in VR headset observation. Once identified, these factors are further discussed and assessed through a series of experiments and usability studies, based on a predefined set of research questions. More specifically, the role of familiarity with the observed place, the role of the environment characteristics shown to the viewer, and the role of the display used for the remote observation of the virtual environment are further investigated. To gain more insights, two usability studies are proposed with the aim of defining guidelines and best practices. The main outcomes from the two studies demonstrate that test users can experience an enhanced realistic observation when natural features, higher resolution displays, natural illumination, and high image contrast are used in Mobile VR. In terms of comfort, simple scene layouts and relaxing environments are considered ideal to reduce visual fatigue and eye strain. Furthermore, sense of presence increases when observed environments induce strong emotions, and depth perception improves in VR when several monocular cues such as lights and shadows are combined with binocular depth cues. Based on these results, this investigation then presents a focused evaluation on the outcomes and introduces an innovative eye-adapted High Dynamic Range (HDR) approach, which the author believes to be of great improvement in the context of remote observation when combined with eye-tracked VR headsets. Within this purpose, a third user study is proposed to compare static HDR and eye-adapted HDR observation in VR, to assess that the latter can improve realism, depth perception, sense of presence, and in certain cases even comfort. Results from this last study confirmed the author expectations, proving that eye-adapted HDR and eye tracking should be used to achieve best visual performances for remote observation in modern VR systems

Tomografia estendida : do básico até o mapeamento de cérebro de camundongos

Orientador: Mateus Borba CardosoTese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb WataghinResumo: Esta tese apresentará uma introdução a imagens de raios-x e como adquirir e processar imagens usando linhas de luz síncrotron. Apresentará os desafios matemáticos e técnicos para reconstruir amostras em três dimensões usando a reconstrução de Tomografia Computadorizada, uma técnica conhecida como CT. Esta técnica tem seu campo de visão limitado ao tamanho da câmera e ao tamanho da iluminação. Uma técnica para ampliar esse campo de visão vai ser apresentada e os desafios técnicos envolvidos para que isso aconteça. Um \textit{pipeline} é proposto e todos os algoritmos necessários foram empacotados em um pacote python chamado Tomosaic. A abordagem baseia-se em adquirir tomogramas parciais em posiçoes pré definidas e depois mesclar os dados em um novo conjunto de dados. Duas maneiras possíveis são apresentadas para essa mescla, uma no domínio das projeções e uma no domínio dos sinogramas. Experimentos iniciais serão então usadas para mostrar que o método proposto funciona com computadores normais. A técnica será aplicada mais tarde para pesquisar a anatomia de cérebros de camundongo completos. Um estudo será apresentado de como obter informação em diferentes escalas do cérebro completo do rato utilizando raios-xAbstract: This thesis will present an introduction to x-ray images and how to acquire and thread images using synchrotron beamlines. It will present the mathematical and technical challenges to reconstruct samples in three dimensions using Computed Tomography reconstruction, a technique known as CT. This technique has a field of view bounded to the camera size and the illumination size. A technique to extended this field of view is going to be presented and the technical challenges involved in order for that to happen will be described. A pipeline is proposed and all the necessary algorithms are contained into a python packaged called Tomosaic. The approach relies on acquired partial tomogram data in a defined grid and later merging the data into a new dataset. Two possible ways are presented in order to that: in the projection domain, and in the sinogram domain. Initial experiments will then be used to show that the pipeline works with normal computers. The technique will be later applied to survey the whole anatomy of whole mouse brains. A study will be shown of how to get the complete range of scales of the mouse brain using x-ray tomography at different resolutionsDoutoradoFísicaDoutor em Ciências163304/2013-01247445/2013, 1456912/2014CNPQCAPE