Development and Application of Semi-automated ITK Tools Development and Application of Semi-automated ITK Tools for the Segmentation of Brain MR Images

Image segmentation is a process to identify regions of interest from digital images. Image segmentation plays an important role in medical image processing which enables a variety of clinical applications. It is also a tool to facilitate the detection of abnormalities such as cancerous lesions in the brain. Although numerous efforts in recent years have advanced this technique, no single approach solves the problem of segmentation for the large variety of image modalities existing today. Consequently, brain MRI segmentation remains a challenging task. The purpose of this thesis is to demonstrate brain MRI segmentation for delineation of tumors, ventricles and other anatomical structures using Insight Segmentation and Registration Toolkit (ITK) routines as the foundation. ITK is an open-source software system to support the Visible Human Project. Visible Human Project is the creation of complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies. Currently under active development, ITK employs leading-edge segmentation and registration algorithms in two, three, and more dimensions. A goal of this thesis is to implement those algorithms to facilitate brain segmentation for a brain cancer research scientist

Improving Semantic Segmentation of 3D Medical Images on CNNs

International audienceA neural network is a mathematical model that is able to perform a task automatically or semi-automatically after learning the human knowledge that we provided. Moreover, a Convolutional Neural Network (CNN) is a type of neural network that has shown to efficiently learn tasks related to the area of image analysis, such as image segmentation, whose main purpose is to find regions or separable objects within an image. A more specific type of segmentation, called semantic segmentation, guarantees that each region has a semantic meaning by giving it a label or class. Since CNNs can automate the task of image semantic segmentation, they have been very useful for the medical area, applying them to the segmentation of organs or abnormalities (tumors). This work aims to improve the task of binary semantic segmentation of volumetric medical images acquired by Magnetic Resonance Imaging (MRI) using a pre-existing Three-Dimensional Convolutional Neural Network (3D CNN) architecture. We propose a formulation of a loss function for training this 3D CNN, for improving pixel-wise segmentation results. This loss function is formulated based on the idea of adapting a similarity coefficient, used for measuring the spatial overlap between the prediction and ground truth, and then using it to train the network. As contribution, the developed approach achieved good performance in a context where the pixel classes are imbalanced. We show how the choice of the loss function for training can affect the final quality of the segmentation. We validate our proposal over two medical image semantic segmentation datasets and show comparisons in performance between the proposed loss function and other pre-existing loss functions used for binary semantic segmentation

Improving of Fingerprint Segmentation Images Based on K-MEANS and DBSCAN Clustering

Nowadays, the fingerprint identification system is the most exploited sector of biometric. Fingerprint image segmentation is considered one of its first processing stage. Thus, this stage affects typically the feature extraction and matching process which leads to fingerprint recognition system with high accuracy. In this paper, three major steps are proposed. First, Soble and TopHat filtering method have been used to improve the quality of the fingerprint images. Then, for each local block in fingerprint image, an accurate separation of the foreground and background region is obtained by K-means clustering for combining 5-dimensional characteristics vector (variance, difference of mean, gradient coherence, ridge direction and energy spectrum). Additionally, in our approach, the local variance thresholding is used to reduce computing time for segmentation. Finally, we are combined to our system DBSCAN clustering which has been performed in order to overcome the drawbacks of K-means classification in fingerprint images segmentation. The proposed algorithm is tested on four different databases. Experimental results demonstrate that our approach is significantly efficacy against some recently published techniques in terms of separation between the ridge and non-ridge region

Automated Three-Dimensional Microbial Sensing and Recognition Using Digital Holography and Statistical Sampling

We overview an approach to providing automated three-dimensional (3D) sensing and recognition of biological micro/nanoorganisms integrating Gabor digital holographic microscopy and statistical sampling methods. For 3D data acquisition of biological specimens, a coherent beam propagates through the specimen and its transversely and longitudinally magnified diffraction pattern observed by the microscope objective is optically recorded with an image sensor array interfaced with a computer. 3D visualization of the biological specimen from the magnified diffraction pattern is accomplished by using the computational Fresnel propagation algorithm. For 3D recognition of the biological specimen, a watershed image segmentation algorithm is applied to automatically remove the unnecessary background parts in the reconstructed holographic image. Statistical estimation and inference algorithms are developed to the automatically segmented holographic image. Overviews of preliminary experimental results illustrate how the holographic image reconstructed from the Gabor digital hologram of biological specimen contains important information for microbial recognition