Segmentation Methods in Biomedical Image Processing

Disertační práce pojednává o moderních metodách a přístupech ke zpracování obrazů, konkrétně k jejich segmentaci, klasifikaci a vyhodnocování parametrů. Jedná se především o zpracování medicínských snímků měkkých tkání pořízených metodou magnetické rezonance (MR) a dále mikroskopických obrazů tkání. Ze segmentovaných obrazů lze jednoduše popsat hranice hledaných objektů. Tyto nalezené hranice mohou sloužit k dalšímu zpracování jako výpočet obvodů, obsahů, povrchů, objemů nebo dokonce k trojrozměrné rekonstrukci zobrazovaného objektu. Popsaná navržená řešení lze použít pro klasifikaci zdravých či postižených tkání snímaných metodami MR či jinými. V disertační práci jsou uvedeny příklady aplikací, ve kterých byly navržené segmentační metody použity. V oblasti segmentace obrazů se práce zaměřuje na metody založené na řešení parciálních diferenciálních rovnic. Jedná se o moderní přístupy zpracování obrazů, zvané též aktivní kontury. Tento přístup ke zpracování obrazů je velmi výhodný u segmentace reálného obrazu, který je zatížený šumem, má neostré hrany a přechody mezi objekty. Výsledkem disertační práce jsou navržené metody pro automatickou segmentaci obrazů a klasifikaci objektů.The PhD thesis deals with modern methods of image processing, especially image segmentation, classification and evaluation of parameters. It is focused primarily on processing medical images of soft tissues obtained by magnetic resonance tomography (MR) and microscopic images of tissues. It is easy to describe edges of the sought objects using of segmented images. The edges found can be useful for further processing of monitored object such as calculating the perimeter, surface and volume evaluation or even three-dimensional shape reconstruction. The proposed solutions can be used for the classification of healthy/unhealthy tissues in MR or other imaging. Application examples of the proposed segmentation methods are shown in this thesis. Research in the area of image segmentation is focused on methods based on solving partial differential equations. This is a modern method for image processing, often called the active contour method. It is of great advantage in the segmentation of real images degraded by noise with fuzzy edges and transitions between objects. The results of the thesis are methods proposed for automatic image segmentation and classification.

Segmentation of perivascular spaces in 7 T MR image using auto-context model with orientation-normalized features

Quantitative study of perivascular spaces (PVSs) in brain magnetic resonance (MR) images is important for understanding the brain lymphatic system and its relationship with neurological diseases. One of major challenges is the accurate extraction of PVSs that have very thin tubular structures with various directions in three-dimensional (3D) MR images. In this paper, we propose a learning-based PVS segmentation method to address this challenge. Specifically, we first determine a region of interest (ROI) by using the anatomical brain structure and the vesselness information derived from eigenvalues of image derivatives. Then, in the ROI, we extract a number of randomized Haar features which are normalized with respect to the principal directions of the underlying image derivatives. The classifier is trained by the random forest model that can effectively learn both discriminative features and classifier parameters to maximize the information gain. Finally, a sequential learning strategy is used to further enforce various contextual patterns around the thin tubular structures into the classifier. For evaluation, we apply our proposed method to the 7T brain MR images scanned from 17 healthy subjects aged from 25 to 37. The performance is measured by voxel-wise segmentation accuracy, cluster- wise classification accuracy, and similarity of geometric properties, such as volume, length, and diameter distributions between the predicted and the true PVSs. Moreover, the accuracies are also evaluated on the simulation images with motion artifacts and lacunes to demonstrate the potential of our method in segmenting PVSs from elderly and patient populations. The experimental results show that our proposed method outperforms all existing PVS segmentation methods

CAD Scheme Based Brain Lesion Segmentation and Classification Approach

Segmentation is a key process in most imaging and classification analysis for Computer-Aided Diagnostic or radiological evaluation (CAD). The pixel based method is a key technique in k-means clustering, as this method is simple and computational complexity is low compared to other region-based or border-based methods. In addition, segmentation of biomedical images using the clustering concept as the number of clusters is known from images of particular regions of human anatomy. The K-means clustering technique is used to track tumor objects in Magnetic Resonance Imaging (MRI). The key concept of the segmentation algorithm is to convert an MR input image into a gradient image and then separate the tumor location in the MR image through the K-media pool. These methods can obtain segmentation of brain images to detect the size and region of the lesion. Therefore, the average k cluster can obtain a robust, effective and accurate segmentation of brain lesions in MRI images automatically and the run time for segmentation of a single lesion is 0.021106. The detection of the tumor and the removal of the magnetic resonance of the brain are performed using the MATLAB software. The automatic instrument is designed to quantify brain tumors using magnetic resonance sets is the main focus of the work. The different methods used for this concept in the content-based recovery system are precision, memory and precision value for visual words, descriptive color and border descriptors, diffused histogram of color and structure. It is expected that the experimental results of the proposed system will produce better results than other existing systems. Total accuracy of 95.6% is obtained using GLCM functions in MATLAB software

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus