PCA Based Bayesian Approach for Automatic Multiple Sclerosis Lesion Detection

The classical Bayes rule plays very important role in the field of lesion identification. However, the Bayesian approach is very difficult in high dimensional spaces for lesion detection. An alternative approach is Principle Component Analysis (PCA) for automatic multiple sclerosis lesion detection problems in high dimensional spaces. In this study, PCA based Bayesian approach is explained for automatic multiple sclerosis lesion detection using Markov Random Fields (MRF)and Singular Value Decomposition (SVD). It is shown that PCA approach provides better understanding of data. Although Bayesian approach gives effective results, itis not easy to use in high dimensional spaces. Therefore, PCA based Bayesian detection will give much more accurate results for automatic multiple sclerosis (MS)lesion detection

Expectation Maximization And Gaussian Model Based Segmentation on Histology Slides

The importance of the Expectation Maximization (EM) algorithm isincreasing day by day in order to solve Maximum A Posteriori (MAP) estimation problems and Gaussian Mixture Models (GMMs), which are parametric probability density functions, have become more popular in computerized applications due tothe EM algorithm. This article explains an automatic GMM based image segmentation method for histology cell images. For this purpose, the GMM parameters, which are recomputed iteratively starting with initial values, arecalculated by using the EM algorithm which classifies each pixel into the class withthe largest probability distribution using maximum likelihood. The accuracy of this segmentation algorithm depends on how much close the probabilistic model to the gray level distributions of the input images

An Automatic Level Set Based Liver Segmentation from MRI Data Sets

A fast and accurate liver segmentation method is a challenging work in medical image analysis area. Liver segmentation is an important process for computer-assisted diagnosis, pre-evaluation of liver transplantation and therapy planning of liver tumors. There are several advantages of magnetic resonance imaging such as free form ionizing radiation and good contrast visualization of soft tissue. Also, innovations in recent technology and image acquisition techniques have made magnetic resonance imaging a major tool in modern medicine. However, the use of magnetic resonance images for liver segmentation has been slow when we compare applications with the central nervous systems and musculoskeletal. The reasons are irregular shape, size and position of the liver, contrast agent effects and similarities of the gray values of neighbor organs. Therefore, in this study, we present a fully automatic liver segmentation method by using an approximation of the level set based contour evolution from T2 weighted magnetic resonance data sets. The method avoids solving partial differential equations and applies only integer operations with a two-cycle segmentation algorithm. The efficiency of the proposed approach is achieved by applying the algorithm to all slices with a constant number of iteration and performing the contour evolution without any user defined initial contour. The obtained results are evaluated with four different similarity measures and they show that the automatic segmentation approach gives successful results

A level set method with Sobolev Gradient and Haralick Edge Detection

Variational level set methods, which have been proposed with various energy functionals, mostly use the ordinary L type gradient in gradient descent algorithm to minimize the energy functional. The gradient flow is influenced by both the energy to be minimized and the norms, which are induced from inner products, used to measure the cost of perturbation of the curve. However, there are many undesired properties related to the gradient flows due to the 2 L type inner products. For example, there is not any regularity term in the definition of this inner product that causes non-smooth flows and inaccurate results. Therefore, in this work, Sobolev gradient has been used that is more efficient than the 2 L type gradient for image segmentation and has powerful properties such as regular gradient flows, independency to parameterization of curves, less sensitive to local features and noise in the image and also faster convergence rate than the standard gradient. In addition, Haralick edge detector has been used instead of the edge indicator function in this study. Because, the traditional edge indicator function, which is the absolute of the gradient of the convolved image with the aussian function, is sensitive to noise in level set methods. Experimental results on real images , which are abdominal magnetic resonance images, have been obtained for spleen and kidney segmentation. Quantitative analyses have been performed by using different measurements to evaluate the performance of the proposed approach, which can ignore topological noises and detect boundaries successfully

Automated Segmentation of HeLa Nuclear Envelope from Electron Microscopy Images

This paper describes an image-processing pipeline for the automatic segmentation of the nuclear envelope of HeLcells observed through Electron Microscopy. The pipeline was applied to a 3D stack of 300 images. The intermediate results of neighbouring slices are further combined to improve the final results. Comparison with a handsegmented ground truth reported Jaccard similarity values between 94-98% on the central slices with a decrease towards the edges of the cell where the structure was considerably more complex. The processing is unsupervised and each 2D slice is processed in about 5-10 seconds running on a MacBook Pro. No systematic attempt to make the code faster was made. These encouraging results could be further used to provide data for more complex segmentation techniques like Deep Learning, which require a considerable amount of data to train architectures like Convolutional Neural Networks. The code is freely available from https://github.com/reyesaldasoro/HeLa-Cell-Segmentatio

Liver segmentation in MRI: a fully automatic method based on stochastic partitions

There are few fully automated methods for liver segmentation in magnetic resonance images (MRI) despite the benefits of this type of acquisition in comparison to other radiology techniques such as computed tomography (CT). Motivated by medical requirements, liver segmentation in MRI has been carried out. For this purpose, we present a new method for liver segmentation based on the watershed transform and stochastic partitions. The classical watershed over-segmentation is reduced using a marker-controlled algorithm. To improve accuracy of selected contours, the gradient of the original image is successfully enhanced by applying a new variant of stochastic watershed. Moreover, a final classifier is performed in order to obtain the final liver mask. Optimal parameters of the method are tuned using a training dataset and then they are applied to the rest of studies (17 datasets). The obtained results (a Jaccard coefficient of 0.91 +/- 0.02) in comparison to other methods demonstrate that the new variant of stochastic watershed is a robust tool for automatic segmentation of the liver in MRI. (C) 2014 Elsevier Ireland Ltd. All rights reserved.This work has been supported by the MITYC under the project NaRALap (ref. TSI-020100-2009-189), partially by the CDTI under the project ONCOTIC (IDI-20101153), by Ministerio de Educacion y Ciencia Spain, Project Game Teen (TIN2010-20187) projects Consolider-C (SEJ2006-14301/PSIC), "CIBER of Physiopathology of Obesity and Nutrition, an initiative of ISCIII" and Excellence Research Program PROMETEO (Generalitat Valenciana. Conselleria de Educacion, 2008-157). We would like to express our gratitude to the Hospital Clinica Benidorm, for providing the MR datasets and to the radiologist team of Inscanner for the manual segmentation of the MR images.López-Mir, F.; Naranjo Ornedo, V.; Angulo, J.; Alcañiz Raya, ML.; Luna, L. (2014). Liver segmentation in MRI: a fully automatic method based on stochastic partitions. Computer Methods and Programs in Biomedicine. 114(1):11-28. https://doi.org/10.1016/j.cmpb.2013.12.022S1128114

Automatic kidney segmentation using Gaussian mixture model on MRI sequences

Robust kidney segmentation from MR images is a very difficult task due to the especially gray level similarity of adjacent organs, partial volume effects and injection of contrast media. In addition to different image characteristics with different MR scanners, the variations of the kidney shapes, gray levels and positions make the identification and segmentation task even harder. In this paper, we propose an automatic kidney segmentation approach using Gaussian mixture model (GMM) that adapts all parameters according to each MR image dataset to handle all these challenging problems. The efficiency in terms of the segmentation performance is achieved by the estimation of the GMM parameters using the Expectation Maximization (EM) method. The segmentation approach is compared to k-means method. The results show that the model based probabilistic segmentation technique gives better performance for both low contrast images and atypical kidney shapes where several algorithms fail on abdominal MR images. © Springer-Verlag Berlin Heidelberg 2011

Fully automated liver segmentation from SPIR image series

Accurate liver segmentation is an important component of surgery planning for liver transplantation, which enables patients with liver disease a chance to survive. Spectral pre-saturation inversion recovery (SPIR) image sequences are useful for liver vessel segmentation because vascular structures in the liver are clearly visible in these sequences. Although level-set based segmentation techniques are frequently used in liver segmentation due to their flexibility to adapt to different problems by incorporating prior knowledge, the need to initialize the contours on each slice is a common drawback of such techniques. In this paper, we present a fully automated variational level set approach for liver segmentation from SPIR image sequences. Our approach is designed to be efficient while achieving high accuracy. The efficiency is achieved by (1) automatically defining an initial contour for each slice, and (2) automatically computing weight values of each term in the applied energy functional at each iteration during evolution. Automated detection and exclusion of spurious structures (e.g. cysts and other bright white regions on the skin) in the pre-processing stage increases the accuracy and robustness. We also present a novel approach to reduce computational cost by employing binary regularization of level set function. A signed pressure force function controls the evolution of the active contour. The method was applied to ten data sets. In each image, the performance of the algorithm was measured using the receiver operating characteristics method in terms of accuracy, sensitivity and specificity. The accuracy of the proposed method was 96%. Quantitative analyses of results indicate that the proposed method can accurately, efficiently and consistently segment liver images. (C) 2014 Elsevier Ltd. All rights reserved