Adaptation and evaluation of the multiple organs OSD for T2 MRI prostate segmentation

International audienceThis paper deals with the adaptation, the tuning and the evaluation of the multiple organs Optimal Surface Detection (OSD) algorithm for the T2 MRI prostate segmentation. This algorithm is initialized by first surface approximations of the prostate (obtained after a model adjustment), the bladder (obtained automatically) and the rectum (interactive geometrical model). These three organs are then segmented together in a multiple organs OSD scheme which proposes a competition between the gray level characteristics and some topological and anatomical information of these three organs. This method has been evaluated on the MICCAI Grand Challenge: Prostate MR Image Segmentation (PROMISE) 2012 training dataset

Incremental Local Linear Fuzzy Classifier in Fisher Space

Optimizing the antecedent part of neurofuzzy system is an active research topic, for which different approaches have been developed. However, current approaches typically suffer from high computational complexity or lack of ability to extract knowledge from a given set of training data. In this paper, we introduce a novel incremental training algorithm for the class of neurofuzzy systems that are structured based on local linear classifiers. Linear discriminant analysis is utilized to transform the data into a space in which linear discriminancy of training samples is maximized. The neurofuzzy classifier is then built in the transformed space, starting from the simplest form (a global linear classifier). If the overall performance of the classifier was not satisfactory, it would be iteratively refined by incorporating additional local classifiers. In addition, rule consequent parameters are optimized using a local least square approach. Our refinement strategy is motivated by LOLIMOT, which is a greedy partition algorithm for structure training and has been successfully applied in a number of identification problems. The proposed classifier is compared to several benchmark classifiers on a number of well-known datasets. The results prove the efficacy of the proposed classifier in achieving high performance while incurring low computational effort

Colony size measurement of the yeast gene deletion strains for functional genomics

BACKGROUND: Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences. RESULTS: Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research. CONCLUSION: GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations

Hybrid-Controlled Neurofuzzy Networks Analysis Resulting in Genetic Regulatory Networks Reconstruction

Reverse engineering of gene regulatory networks (GRNs) is the process of estimating genetic interactions of a cellular system from gene expression data. In this paper, we propose a novel hybrid systematic algorithm based on neurofuzzy network for reconstructing GRNs from observational gene expression data when only a medium-small number of measurements are available. The approach uses fuzzy logic to transform gene expression values into qualitative descriptors that can be evaluated by using a set of defined rules. The algorithm uses neurofuzzy network to model genes effects on other genes followed by four stages of decision making to extract gene interactions. One of the main features of the proposed algorithm is that an optimal number of fuzzy rules can be easily and rapidly extracted without overparameterizing. Data analysis and simulation are conducted on microarray expression profiles of S. cerevisiae cell cycle and demonstrate that the proposed algorithm not only selects the patterns of the time series gene expression data accurately, but also provides models with better reconstruction accuracy when compared with four published algorithms: DBNs, VBEM, time delay ARACNE, and PF subjected to LASSO. The accuracy of the proposed approach is evaluated in terms of recall and F-score for the network reconstruction task

Optimized Multichannel Filter Bank with Flat Frequency Response for Texture Segmentation

<p/> <p>Previous approaches to texture analysis and segmentation use multichannel filtering by applying a set of filters in the frequency domain or a set of masks in the spatial domain. This paper presents two new texture segmentation algorithms based on multichannel filtering in conjunction with neural networks for feature extraction and segmentation. The features extracted by Gabor filters have been applied for image segmentation and analysis. Suitable choices of filter parameters and filter bank coverage in the frequency domain to optimize the filters are discussed. Here we introduce two methods to optimize Gabor filter bank. First, a Gabor filter bank with a flat response is implemented and the optimal feature dimension is extracted by competitive networks. Second, a subset of Gabor filter bank is selected to compose the best discriminative filters, so that each filter in this small set can discriminate a pair of textures in a given image. In both approaches, multilayer perceptrons are employed to segment the extracted features. The comparisons of segmentation results generated using the proposed methods and previous research using Gabor, discrete cosine transform (DCT), and Laws filters are presented. Finally, the segmentation results generated by applying the optimized filter banks to textured images are presented and discussed.</p

Neural Network based Segmentation of Magnetic Resonance Images of the Brain

This paper presents a study investigating the potential of artificial neural networks (ANN&apos;s) for the classification and segmentation of magnetic resonance (MR) images of the human brain. In this study, we present the application of a Learning Vector Quantization (LVQ) Artificial Neural Network (ANN) for the multispectral supervised classification of MR images. We have modified the LVQ for better and more accurate classification. We have compared the results using LVQ ANN versus back-propagation ANN. This comparison shows that, unlike back-propagation ANN, our method is insensitive to the gray-level variation of MR images between different slices. It shows that tissue segmentation using LVQ ANN also performs better and faster than that using back-propagation ANN. I. Introduction Segmentation of images obtained from magnetic resonance (MR) imaging techniques is an important step in the analysis of MR images of the human body. MR imaging has a unique advantage over other modalities in t..

Edge focused super-resolution of thermal images

International audienceIn this work, a super-resolution method is proposed for indoor scenes captured by low-resolution thermal cameras. The proposed method is called Edge Focused Thermal Super-resolution (EFTS) which contains an edge extraction module enforcing the neural networks to focus on the edge of images. Utilizing edge information, our model, based on residual dense blocks, can perform super-resolution for thermal images, while enhancing the visual information of the edges. Experiments on benchmark datasets showed that our EFTS method achieves better performance in comparison to the state-of-the-art techniques