Unsupervised cell segmentation and labelling in neural tissue images

Neurodegenerative diseases are a group of largely incurable disorders characterised by the progressive loss of neurons and for which often the molecular mechanisms are poorly understood. To bridge this gap, researchers employ a range of techniques. A very prominent and useful technique adopted across many different fields is imaging and the analysis of histopathological and fluorescent label tissue samples. Although image acquisition has been efficiently automated recently, automated analysis still presents a bottleneck. Although various methods have been developed to automate this task, they tend to make use of single-purpose machine learning models that require extensive training, imposing a significant workload on the experts and introducing variability in the analysis. Moreover, these methods are impractical to audit and adapt, as their internal parameters are difficult to interpret and change. Here, we present a novel unsupervised automated schema for object segmentation of images, exemplified on a dataset of tissue images. Our schema does not require training data, can be fully audited and is based on a series of understandable biological decisions. In order to evaluate and validate our schema, we compared it with a state-of-the-art automated segmentation method for post-mortem tissues of ALS patients

GPU acceleration of edge detection algorithm based on local variance and integral image: application to air bubbles boundaries extraction

Accurate detection of air bubbles boundaries is of crucial importance in determining the performance and in the study of various gas/liquid two-phase flow systems. The main goal of this Accurate detection of air bubbles boundaries is of crucial importance in determining the performance and in the study of various gas/liquid two-phase flow systems. The main goal of this Accurate detection of air bubbles boundaries is of crucial importance in determining the performance and in the study of various gas/liquid two-phase flow systems. The main goal of this work is edge extraction of air bubbles rising in two-phase flow in real-time. To accomplish this, a fast algorithm based on local variance is improved and accelerated on the GPU to detect bubble contour. The proposed method is robust against changes of intensity contrast of edges and capable of giving high detection responses on low contrast edges. This algorithm is performed in two steps: in the first step, the local variance of each pixel is computed based on integral image, and then the resulting contours are thinned to generate the final edge map. We have implemented our algorithm on an NVIDIA GTX 780 GPU. The parallel implementation of our algorithm gives a speedup factor equal to 17x for high resolution images (1024×1024 pixels) compared to the serial implementation. Also, quantitative and qualitative assessments of our algorithm versus the most common edge detection algorithms from the literature were performed. A remarkable performance in terms of results accuracy and computation time is achieved with our algorithm. work is edge extraction of air bubbles rising in two-phase flow in real-time. To accomplish this, a fast algorithm based on local variance is improved and accelerated on the GPU to detect bubble contour. The proposed method is robust against changes of intensity contrast of edges and capable of giving high detection responses on low contrast edges. This algorithm is performed in two steps: in the first step, the local variance of each pixel is computed based on integral image, and then the resulting contours are thinned to generate the final edge map. We have implemented our algorithm on an NVIDIA GTX 780 GPU. The parallel implementation of our algorithm gives a speedup factor equal to 17x for high resolution images (1024×1024 pixels) compared to the serial implementation. Also, quantitative and qualitative assessments of our algorithm versus the most common edge detection algorithms from the literature were performed. A remarkable performance in terms of results accuracy and computation time is achieved with our algorithm. work is edge extraction of air bubbles rising in two-phase flow in real-time. To accomplish this, a fast algorithm based on local variance is improved and accelerated on the GPU to detect bubble contour. The proposed method is robust against changes of intensity contrast of edges and capable of giving high detection responses on low contrast edges. This algorithm is performed in two steps: in the first step, the local variance of each pixel is computed based on integral image, and then the resulting contours are thinned to generate the final edge map. We have implemented our algorithm on an NVIDIA GTX 780 GPU. The parallel implementation of our algorithm gives a speedup factor equal to 17x for high resolution images (1024×1024 pixels) compared to the serial implementation. Also, quantitative and qualitative assessments of our algorithm versus the most common edge detection algorithms from the literature were performed. A remarkable performance in terms of results accuracy and computation time is achieved with our algorithm

Proposta de uma plataforma de imageamento microscópico portátil baseada em holografia digital inline

Orientador : Prof. Dr. Aldo Von WangenheimTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 29/01/2015Inclui referênciasResumo: Nesta tese o desenvolvimento de tecnologias de imageamento sem-lentes utilizando o conceito de holografia digital inline para o enfoque microscópico é apresentado. Na formação de imagem sem lentes, o princípio do imageamento por sombras é utilizado, onde as amostras são iluminadas por uma fonte de luz, e sombras contendo as assinaturas das partículas no plano-objeto são projetadas e capturadas em um meio detector eletrônico. Pelo uso de um sistema espacialmente e temporalmente coerente de iluminação, o princípio da difração de onda é aplicado, e assinaturas de padrões de interferências holográficas são projetadas ao invés de somente sombras com assinaturas espaciais. Este conceito denomina-se de holografia digital inline, e métodos numéricos são requeridos para a conversão do sinal holográfico em informação morfológica do plano-objeto. Embora explorada bastante recentemente, a holografia digital inline possibilita horizontes para uma vasta gama de aplicações que envolvem a miniaturização de microscópios em plataformas portáteis, que por sua vez são facilmente integradas com recursos computacionais. Nesta tese de doutorado são propostas 2 plataformas distintas baseadas em holografia digital inline: (i) plataforma holográfica com melhoramento da resolução das assinaturas holográficas por meio de técnicas de super-resolução, (ii) plataforma holográfica para o processamento de vídeo em altas taxas de amostragem. A primeira plataforma é baseada na premissa do deslocamento da fonte luminosa, realizando a computação de uma imagem holográfica em alta-resolução a partir de um conjunto de múltiplas observações da mesma cena. Métodos de registro das imagens holográficas são utilizados, seguidos por um procedimento de otimização do alinhamento inspirado em modelos variacionais de energia. Um framework bio-inspirado é utilizado para minimizar a função em relação a um termo de fidelidade e uma medida de sharpness, e encontrar a solução de ótimo global de alinhamento das imagens. A cena é aproximadamente planar, e somente amostras estáticas são utilizadas neste contexto. Para os hologramas em alta-resolução, métodos computacionais numéricos baseados em recuperação de fase são aplicados para difração do sinal de onda e recuperar as informações geométricas da amostra analisada. A plataforma holográfica foi validada com amostras biológicas de células humanas reprodutoras masculinas, onde a confirmação microscópica foi obtida através de um microscópio óptico convencional, apresentando alta correlação com a imagem de campo de brilho (bright-field ). Os resultados obtidos mostram uma resolução espacial de ?1?m sobre um campo máximo de visão de ?30mm2. Diferentemente das abordagens descritas da literatura, somente uma fonte de iluminação é utilizada para melhoramento da resolução, bem como os métodos de registro e minimização são especificamente designados para incrementar o sinal holográfico da propagação da onda. A segunda plataforma apresenta como enfoque a visualização de amostras biológicas in-situ, como uma ferramenta de propósito geral de imageamento em meio fluídico. A plataforma para vídeo holográfico é mais simples que a plataforma com melhoramento de resolução, e esta pode ser miniaturizada em apenas alguns centímetros cúbicos com resolução de algumas frações de micrômetros. Os experimentos nesta plataforma foram conduzidos principalmente na inspeção de micro-organismos existentes em amostras de água, onde uma série de espécimens podem ser verificados. A vantagem de uma plataforma holográfica em vídeo é o imageamento de estruturas em 4D (volume e tempo), onde um simples vídeo pode ser analisado repetidamente em diferentes pontos de difração. Palavras-chave: Holografia Digital inline, Super-Resolução em Multi-Frame, Vídeo Holográfico, Plataformas de Diagnóstico em Point-of-Care, Imageamento Sem-Lentes.Abstract: In this doctoral's dissertation, lensless imaging technologies based on the digital inline holography concept were developed for the biological microscopy context. From a lensless image formation point-of-view, the shadow imaging principle is used, where the samples are illuminated by a light-source, and shadows containing particle's signatures are projected from the object-plane to an electronic detector. By using a temporal and spatial coherent illumination system, the diffraction-wave principle is applied, and interference holographic patterns are projected, instead of simple spatial signature shadows only. This concept is the so-called digital inline holography, and numerical methods should be used to convert holographic signals into morphological details of the object-plane. Digital inline holography has been explored very recently, opening a wide range of new applications involving the miniaturization of imaging devices into portable platforms, that can be easily integrated with computational resources. In this doctoral's dissertation two distinct platforms based on digital inline holography are presented: (i) holographic platform based on resolution improvement of the holographic signatures, (ii) holographic platform for video processing using high-frame rate sampling. The first platform is based on the premise of computing a higher resolution holographic image from a set of multiple observations of the scene. Image registration methods for the holographic images are used, followed by an optimization approach inspired on variational models of energy equation. A bio-inspired framework is used to minimize this function based on a fidelity term and a sharpness measure, and its minimization is used to find a global optimum solution for the alignment problem. The scene is approximately planar, and static samples can be imaged in this platform. For the high-resolution holograms, numerical diffraction methods are used to recover the phase information, and consequently the morphological information of the analyzed sample. The holographic platform was validated using biological human samples corresponding to reproductive male cells (sperm) using a conventional optical microscope, showing a high correlation with the bright-field microscopy image. The obtained results show a spatial resolution of ?1?m in a field-of-view corresponding to ?30mm2. Differently from the state-of-the-art approaches, this method is based on a single shifted light-source where arbitrary displacements are registered into a single frame, using a combined optimization approach. The second approach has the biological visualization of in-situ specimens in focus. This platform is presented as a generic tool for the visualization of live microorganism in a fluidic mean, being simpler than the previously described platform. On the other hand, this platform can be easily miniaturized into a few cubic centimetres, having resolution of a few microns. Experimental results in this platform were conducted based on the inspection of free-living microorganism in water samples, where several specimens can be observed. A goal of this video holographic platform is the 4D imaging (volume over time), where a single captured video can be repeatedly analyzed for different object-plane diffraction distances. Keywords: Digital Inline Holography, Multi-Frame Super-Resolution, Holographic Video, Point-of-Care Diagnostic Platforms, Lensless Imaging