End-to-End Learned Random Walker for Seeded Image Segmentation

We present an end-to-end learned algorithm for seeded segmentation. Our method is based on the Random Walker algorithm, where we predict the edge weights of the underlying graph using a convolutional neural network. This can be interpreted as learning context-dependent diffusivities for a linear diffusion process. Besides calculating the exact gradient for optimizing these diffusivities, we also propose simplifications that sparsely sample the gradient and still yield competitive results. The proposed method achieves the currently best results on a seeded version of the CREMI neuron segmentation challenge

Seeking multi-thresholds for image segmentation with Learning Automata

This paper explores the use of the Learning Automata (LA) algorithm to compute threshold selection for image segmentation as it is a critical preprocessing step for image analysis, pattern recognition and computer vision. LA is a heuristic method which is able to solve complex optimization problems with interesting results in parameter estimation. Despite other techniques commonly seek through the parameter map, LA explores in the probability space providing appropriate convergence properties and robustness. The segmentation task is therefore considered as an optimization problem and the LA is used to generate the image multi-threshold separation. In this approach, one 1D histogram of a given image is approximated through a Gaussian mixture model whose parameters are calculated using the LA algorithm. Each Gaussian function approximating the histogram represents a pixel class and therefore a threshold point. The method shows fast convergence avoiding the typical sensitivity to initial conditions such as the Expectation Maximization (EM) algorithm or the complex time-consuming computations commonly found in gradient methods. Experimental results demonstrate the algorithm ability to perform automatic multi-threshold selection and show interesting advantages as it is compared to other algorithms solving the same task.Comment: 22 Pages. arXiv admin note: text overlap with arXiv:1405.722

Semantic Segmentation of Human Thigh Quadriceps Muscle in Magnetic Resonance Images

This paper presents an end-to-end solution for MRI thigh quadriceps segmentation. This is the first attempt that deep learning methods are used for the MRI thigh segmentation task. We use the state-of-the-art Fully Convolutional Networks with transfer learning approach for the semantic segmentation of regions of interest in MRI thigh scans. To further improve the performance of the segmentation, we propose a post-processing technique using basic image processing methods. With our proposed method, we have established a new benchmark for MRI thigh quadriceps segmentation with mean Jaccard Similarity Index of 0.9502 and processing time of 0.117 second per image.Comment: 27 pages, 7 figures and 5 table

Learning Object Localization and 6D Pose Estimation from Simulation and Weakly Labeled Real Images

This work proposes a process for efficiently training a point-wise object detector that enables localizing objects and computing their 6D poses in cluttered and occluded scenes. Accurate pose estimation is typically a requirement for robust robotic grasping and manipulation of objects placed in cluttered, tight environments, such as a shelf with multiple objects. To minimize the human labor required for annotation, the proposed object detector is first trained in simulation by using automatically annotated synthetic images. We then show that the performance of the detector can be substantially improved by using a small set of weakly annotated real images, where a human provides only a list of objects present in each image without indicating the location of the objects. To close the gap between real and synthetic images, we adopt a domain adaptation approach through adversarial training. The detector resulting from this training process can be used to localize objects by using its per-object activation maps. In this work, we use the activation maps to guide the search of 6D poses of objects. Our proposed approach is evaluated on several publicly available datasets for pose estimation. We also evaluated our model on classification and localization in unsupervised and semi-supervised settings. The results clearly indicate that this approach could provide an efficient way toward fully automating the training process of computer vision models used in robotics

A survey of non-exchangeable priors for Bayesian nonparametric models

Dependent nonparametric processes extend distributions over measures, such as the Dirichlet process and the beta process, to give distributions over collections of measures, typically indexed by values in some covariate space. Such models are appropriate priors when exchangeability assumptions do not hold, and instead we want our model to vary fluidly with some set of covariates. Since the concept of dependent nonparametric processes was formalized by MacEachern [1], there have been a number of models proposed and used in the statistics and machine learning literatures. Many of these models exhibit underlying similarities, an understanding of which, we hope, will help in selecting an appropriate prior, developing new models, and leveraging inference techniques

Discovery Radiomics for Multi-Parametric MRI Prostate Cancer Detection

Prostate cancer is the most diagnosed form of cancer in Canadian men, and is the third leading cause of cancer death. Despite these statistics, prognosis is relatively good with a sufficiently early diagnosis, making fast and reliable prostate cancer detection crucial. As imaging-based prostate cancer screening, such as magnetic resonance imaging (MRI), requires an experienced medical professional to extensively review the data and perform a diagnosis, radiomics-driven methods help streamline the process and has the potential to significantly improve diagnostic accuracy and efficiency, and thus improving patient survival rates. These radiomics-driven methods currently rely on hand-crafted sets of quantitative imaging-based features, which are selected manually and can limit their ability to fully characterize unique prostate cancer tumour phenotype. In this study, we propose a novel \textit{discovery radiomics} framework for generating custom radiomic sequences tailored for prostate cancer detection. Discovery radiomics aims to uncover abstract imaging-based features that capture highly unique tumour traits and characteristics beyond what can be captured using predefined feature models. In this paper, we discover new custom radiomic sequencers for generating new prostate radiomic sequences using multi-parametric MRI data. We evaluated the performance of the discovered radiomic sequencer against a state-of-the-art hand-crafted radiomic sequencer for computer-aided prostate cancer detection with a feedforward neural network using real clinical prostate multi-parametric MRI data. Results for the discovered radiomic sequencer demonstrate good performance in prostate cancer detection and clinical decision support relative to the hand-crafted radiomic sequencer. The use of discovery radiomics shows potential for more efficient and reliable automatic prostate cancer detection.Comment: 8 page

Probabilistic tractography, Path Integrals and the Fokker Planck equation

Probabilistic tractography based on diffusion weighted MRI has become a powerful approach for quantifying structural brain connectivities. In several works the similarity of probabilistic tractography and path integrals was already pointed out. This work investigates this connection more closely. For the so called Wiener process, a Gaussian random walker, the equivalence is worked out. We identify the source of the asymmetry of usual random walkers approaches and show that there is a proper symmetrization, which leads to a new symmetric connectivity measure. To compute this measure we will use the Fokker-Planck equation, which is an equivalent representation of a Wiener process in terms of a partial differential equation. In experiments we show that the proposed approach leads a symmetric and robust connectivity measure

Analytical tools for single-molecule fluorescence imaging in cellulo

Recent technological advances in cutting-edge ultrasensitive fluorescence microscopy have allowed single-molecule imaging experiments in living cells across all three domains of life to become commonplace. Single-molecule live-cell data is typically obtained in a low signal-to-noise ratio (SNR) regime sometimes only marginally in excess of 1, in which a combination of detector shot noise, sub-optimal probe photophysics, native cell autofluorescence and intrinsically underlying stochastic of molecules result in highly noisy datasets for which underlying true molecular behaviour is non-trivial to discern. The ability to elucidate real molecular phenomena is essential in relating experimental single-molecule observations to both the biological system under study as well as offering insight into the fine details of the physical and chemical environments of the living cell. To confront this problem of faithful signal extraction and analysis in a noise-dominated regime, the needle in a haystack challenge, such experiments benefit enormously from a suite of objective, automated, high-throughput analysis tools that can home in on the underlying molecular signature and generate meaningful statistics across a large population of individual cells and molecules. Here, I discuss the development and application of several analytical methods applied to real case studies, including objective methods of segmenting cellular images from light microscopy data, tools to robustly localize and track single fluorescently-labelled molecules, algorithms to objectively interpret molecular mobility, analysis protocols to reliably estimate molecular stoichiometry and turnover, and methods to objectively render distributions of molecular parameter

A dense subgraph based algorithm for compact salient image region detection

We present an algorithm for graph based saliency computation that utilizes the underlying dense subgraphs in finding visually salient regions in an image. To compute the salient regions, the model first obtains a saliency map using random walks on a Markov chain. Next, k-dense subgraphs are detected to further enhance the salient regions in the image. Dense subgraphs convey more information about local graph structure than simple centrality measures. To generate the Markov chain, intensity and color features of an image in addition to region compactness is used. For evaluating the proposed model, we do extensive experiments on benchmark image data sets. The proposed method performs comparable to well-known algorithms in salient region detection.Comment: 33 pages, 18 figures, Single column manuscript pre-print, Accepted at Computer Vision and Image Understanding, Elsevie

RANSAC: Identification of Higher-Order Geometric Features and Applications in Humanoid Robot Soccer

The ability for an autonomous agent to self-localise is directly proportional to the accuracy and precision with which it can perceive salient features within its local environment. The identification of such features by recognising geometric profile allows robustness against lighting variations, which is necessary in most industrial robotics applications. This paper details a framework by which the random sample consensus (RANSAC) algorithm, often applied to parameter fitting in linear models, can be extended to identify higher-order geometric features. Goalpost identification within humanoid robot soccer is investigated as an application, with the developed system yielding an order-of-magnitude improvement in classification performance relative to a traditional histogramming methodology.Comment: 8 pages, 6 figure