Human mobility monitoring in very low resolution visual sensor network

This paper proposes an automated system for monitoring mobility patterns using a network of very low resolution visual sensors (30 30 pixels). The use of very low resolution sensors reduces privacy concern, cost, computation requirement and power consumption. The core of our proposed system is a robust people tracker that uses low resolution videos provided by the visual sensor network. The distributed processing architecture of our tracking system allows all image processing tasks to be done on the digital signal controller in each visual sensor. In this paper, we experimentally show that reliable tracking of people is possible using very low resolution imagery. We also compare the performance of our tracker against a state-of-the-art tracking method and show that our method outperforms. Moreover, the mobility statistics of tracks such as total distance traveled and average speed derived from trajectories are compared with those derived from ground truth given by Ultra-Wide Band sensors. The results of this comparison show that the trajectories from our system are accurate enough to obtain useful mobility statistics

Dynamical models and machine learning for supervised segmentation

This thesis is concerned with the problem of how to outline regions of interest in medical images, when the boundaries are weak or ambiguous and the region shapes are irregular. The focus on machine learning and interactivity leads to a common theme of the need to balance conflicting requirements. First, any machine learning method must strike a balance between how much it can learn and how well it generalises. Second, interactive methods must balance minimal user demand with maximal user control. To address the problem of weak boundaries,methods of supervised texture classification are investigated that do not use explicit texture features. These methods enable prior knowledge about the image to benefit any segmentation framework. A chosen dynamic contour model, based on probabilistic boundary tracking, combines these image priors with efficient modes of interaction. We show the benefits of the texture classifiers over intensity and gradient-based image models, in both classification and boundary extraction. To address the problem of irregular region shape, we devise a new type of statistical shape model (SSM) that does not use explicit boundary features or assume high-level similarity between region shapes. First, the models are used for shape discrimination, to constrain any segmentation framework by way of regularisation. Second, the SSMs are used for shape generation, allowing probabilistic segmentation frameworks to draw shapes from a prior distribution. The generative models also include novel methods to constrain shape generation according to information from both the image and user interactions. The shape models are first evaluated in terms of discrimination capability, and shown to out-perform other shape descriptors. Experiments also show that the shape models can benefit a standard type of segmentation algorithm by providing shape regularisers. We finally show how to exploit the shape models in supervised segmentation frameworks, and evaluate their benefits in user trials

Contributions to the study of Austism Spectrum Brain conectivity

164 p.Autism Spectrum Disorder (ASD) is a largely prevalent neurodevelopmental condition with a big social and economical impact affecting the entire life of families. There is an intense search for biomarkers that can be assessed as early as possible in order to initiate treatment and preparation of the family to deal with the challenges imposed by the condition. Brain imaging biomarkers have special interest. Specifically, functional connectivity data extracted from resting state functional magnetic resonance imaging (rs-fMRI) should allow to detect brain connectivity alterations. Machine learning pipelines encompass the estimation of the functional connectivity matrix from brain parcellations, feature extraction and building classification models for ASD prediction. The works reported in the literature are very heterogeneous from the computational and methodological point of view. In this Thesis we carry out a comprehensive computational exploration of the impact of the choices involved while building these machine learning pipelines

Cancer Outcome Prediction with Multiform Medical Data using Deep Learning

This thesis illustrated the work done for my PhD project, which aims to develop personalised cancer outcome prediction models using various types of medical data. A predictive modelling workflow that can analyse data with different forms and generate comprehensive outcome prediction was designed and implemented on a variety of datasets. The model development was accompanied by applying deep learning techniques for multivariate survival analysis, medical image analysis and sequential data processing. The modelling workflow was applied to three different tasks: 1. Deep learning models were developed for estimating the progression probability of patients with colorectal cancer after resection and after different lines of chemotherapy, which got significantly better predictive performance than the Cox regression models. Besides, CT-based models were developed for predicting the tumour local response after chemotherapy of patients with lung metastasis, which got an AUC of 0. 769 on disease progression detection and 0.794 on treatment response classification. 2. Deep learning models were developed for predicting the survival state of patients with non-small cell lung cancer after radiotherapy using CT scans, dose distribution and disease and treatment variables. The eventual model obtained by ensemble voting got an AUC of 0.678, which is significantly higher than the score achieved by the radiomics model (0.633). 3. Deep-learning-aided approaches were used for estimating the progression risk for patients with solitary fibrous tumours using digital pathology slides. The deep learning architecture was able to optimise the WHO risk assessment model using automatically identified levels of mitotic activity. Compared to manual counting given by pathologists, deep-learning-aided mitosis counting can re-grade the patients whose risks were underestimated. The applications proved that the predictive models based on hybrid neural networks were able to analyse multiform medical data for generating data-based cancer outcome prediction. The results can be used for realising personalised treatment planning, evaluating treatment quality, and aiding clinical decision-making

Super resolution and dynamic range enhancement of image sequences

Camera producers try to increase the spatial resolution of a camera by reducing size of sites on sensor array. However, shot noise causes the signal to noise ratio drop as sensor sites get smaller. This fact motivates resolution enhancement to be performed through software. Super resolution (SR) image reconstruction aims to combine degraded images of a scene in order to form an image which has higher resolution than all observations. There is a demand for high resolution images in biomedical imaging, surveillance, aerial/satellite imaging and high-definition TV (HDTV) technology. Although extensive research has been conducted in SR, attention has not been given to increase the resolution of images under illumination changes. In this study, a unique framework is proposed to increase the spatial resolution and dynamic range of a video sequence using Bayesian and Projection onto Convex Sets (POCS) methods. Incorporating camera response function estimation into image reconstruction allows dynamic range enhancement along with spatial resolution improvement. Photometrically varying input images complicate process of projecting observations onto common grid by violating brightness constancy. A contrast invariant feature transform is proposed in this thesis to register input images with high illumination variation. Proposed algorithm increases the repeatability rate of detected features among frames of a video. Repeatability rate is increased by computing the autocorrelation matrix using the gradients of contrast stretched input images. Presented contrast invariant feature detection improves repeatability rate of Harris corner detector around %25 on average. Joint multi-frame demosaicking and resolution enhancement is also investigated in this thesis. Color constancy constraint set is devised and incorporated into POCS framework for increasing resolution of color-filter array sampled images. Proposed method provides fewer demosaicking artifacts compared to existing POCS method and a higher visual quality in final image

Graph Spectral Image Processing

Recent advent of graph signal processing (GSP) has spurred intensive studies of signals that live naturally on irregular data kernels described by graphs (e.g., social networks, wireless sensor networks). Though a digital image contains pixels that reside on a regularly sampled 2D grid, if one can design an appropriate underlying graph connecting pixels with weights that reflect the image structure, then one can interpret the image (or image patch) as a signal on a graph, and apply GSP tools for processing and analysis of the signal in graph spectral domain. In this article, we overview recent graph spectral techniques in GSP specifically for image / video processing. The topics covered include image compression, image restoration, image filtering and image segmentation

Brain Tumor Detection and Segmentation in Multisequence MRI

Tato práce se zabývá detekcí a segmentací mozkového nádoru v multisekvenčních MR obrazech se zaměřením na gliomy vysokého a nízkého stupně malignity. Jsou zde pro tento účel navrženy tři metody. První metoda se zabývá detekcí prezence částí mozkového nádoru v axiálních a koronárních řezech. Jedná se o algoritmus založený na analýze symetrie při různých rozlišeních obrazu, který byl otestován na T1, T2, T1C a FLAIR obrazech. Druhá metoda se zabývá extrakcí oblasti celého mozkového nádoru, zahrnující oblast jádra tumoru a edému, ve FLAIR a T2 obrazech. Metoda je schopna extrahovat mozkový nádor z 2D i 3D obrazů. Je zde opět využita analýza symetrie, která je následována automatickým stanovením intenzitního prahu z nejvíce asymetrických částí. Třetí metoda je založena na predikci lokální struktury a je schopna segmentovat celou oblast nádoru, jeho jádro i jeho aktivní část. Metoda využívá faktu, že většina lékařských obrazů vykazuje vysokou podobnost intenzit sousedních pixelů a silnou korelaci mezi intenzitami v různých obrazových modalitách. Jedním ze způsobů, jak s touto korelací pracovat a používat ji, je využití lokálních obrazových polí. Podobná korelace existuje také mezi sousedními pixely v anotaci obrazu. Tento příznak byl využit v predikci lokální struktury při lokální anotaci polí. Jako klasifikační algoritmus je v této metodě použita konvoluční neuronová síť vzhledem k její známe schopnosti zacházet s korelací mezi příznaky. Všechny tři metody byly otestovány na veřejné databázi 254 multisekvenčních MR obrazech a byla dosáhnuta přesnost srovnatelná s nejmodernějšími metodami v mnohem kratším výpočetním čase (v řádu sekund při použitý CPU), což poskytuje možnost manuálních úprav při interaktivní segmetaci.This work deals with the brain tumor detection and segmentation in multisequence MR images with particular focus on high- and low-grade gliomas. Three methods are propose for this purpose. The first method deals with the presence detection of brain tumor structures in axial and coronal slices. This method is based on multi-resolution symmetry analysis and it was tested for T1, T2, T1C and FLAIR images. The second method deals with extraction of the whole brain tumor region, including tumor core and edema, in FLAIR and T2 images and is suitable to extract the whole brain tumor region from both 2D and 3D. It also uses the symmetry analysis approach which is followed by automatic determination of the intensity threshold from the most asymmetric parts. The third method is based on local structure prediction and it is able to segment the whole tumor region as well as tumor core and active tumor. This method takes the advantage of a fact that most medical images feature a high similarity in intensities of nearby pixels and a strong correlation of intensity profiles across different image modalities. One way of dealing with -- and even exploiting -- this correlation is the use of local image patches. In the same way, there is a high correlation between nearby labels in image annotation, a feature that has been used in the ``local structure prediction'' of local label patches. Convolutional neural network is chosen as a learning algorithm, as it is known to be suited for dealing with correlation between features. All three methods were evaluated on a public data set of 254 multisequence MR volumes being able to reach comparable results to state-of-the-art methods in much shorter computing time (order of seconds running on CPU) providing means, for example, to do online updates when aiming at an interactive segmentation.