A Hybrid Approach of Using Particle Swarm Optimization and Volumetric Active Contour without Edge for Segmenting Brain Tumors in MRI Scan

Segmentation of brain tumors in magnetic resonance imaging is a one of the most complex processes in medical image analysis because it requires a combination of data knowledge with domain knowledge to achieve highly results. Such that, the data knowledge refers to homogeneity, continuity, and anatomical texture. While the domain knowledge refers to shapes, location, and size of the tumor to be delineated. Due to recent advances in medical imaging technologies which produce a massive number of cross-sectional slices, this makes a manual segmentation process is a very intensive, time-consuming and prone to inconsistences. In this study, an automated method for recognizing and segmenting the pathological area in MRI scans has been developed. First the dataset has been pre-processed and prepared by implementing a set of algorithms to standardize all collected samples. A particle swarm optimization is utilized to find the core of pathological area within each MRI slice. Finally, an active contour without edge method is utilized to extract the pathological area in MRI scan. Results reported on the collected dataset includes 50 MRI scans of pathological patients that was provided by Iraqi Center for Research and Magnetic Resonance of Al Imamain Al-Kadhimain Medical City in Iraq. The achieved accuracy of the proposed method was 92% compared with manual delineation

Fully-automated μMRI morphometric phenotyping of the Tc1 mouse model of Down Syndrome

We describe a fully automated pipeline for the morphometric phenotyping of mouse brains from μMRI data, and show its application to the Tc1 mouse model of Down syndrome, to identify new morphological phenotypes in the brain of this first transchromosomic animal carrying human chromosome 21. We incorporate an accessible approach for simultaneously scanning multiple ex vivo brains, requiring only a 3D-printed brain holder, and novel image processing steps for their separation and orientation. We employ clinically established multi-atlas techniques-superior to single-atlas methods-together with publicly-available atlas databases for automatic skull-stripping and tissue segmentation, providing high-quality, subject-specific tissue maps. We follow these steps with group-wise registration, structural parcellation and both Voxel- and Tensor-Based Morphometry-advantageous for their ability to highlight morphological differences without the laborious delineation of regions of interest. We show the application of freely available open-source software developed for clinical MRI analysis to mouse brain data: NiftySeg for segmentation and NiftyReg for registration, and discuss atlases and parameters suitable for the preclinical paradigm. We used this pipeline to compare 29 Tc1 brains with 26 wild-type littermate controls, imaged ex vivo at 9.4T. We show an unexpected increase in Tc1 total intracranial volume and, controlling for this, local volume and grey matter density reductions in the Tc1 brain compared to the wild-types, most prominently in the cerebellum, in agreement with human DS and previous histological findings

Functional and structural MRI image analysis for brain glial tumors treatment

Cotutela con il Dipartimento di Biotecnologie e Scienze della Vita, Universiità degli Studi dell'Insubria.openThis Ph.D Thesis is the outcome of a close collaboration between the Center for Research in Image Analysis and Medical Informatics (CRAIIM) of the Insubria University and the Operative Unit of Neurosurgery, Neuroradiology and Health Physics of the University Hospital ”Circolo Fondazione Macchi”, Varese. The project aim is to investigate new methodologies by means of whose, develop an integrated framework able to enhance the use of Magnetic Resonance Images, in order to support clinical experts in the treatment of patients with brain Glial tumor. Both the most common uses of MRI technology for non-invasive brain inspection were analyzed. From the Functional point of view, the goal has been to provide tools for an objective reliable and non-presumptive assessment of the brain’s areas locations, to preserve them as much as possible at surgery. From the Structural point of view, methodologies for fully automatic brain segmentation and recognition of the tumoral areas, for evaluating the tumor volume, the spatial distribution and to be able to infer correlation with other clinical data or trace growth trend, have been studied. Each of the proposed methods has been thoroughly assessed both qualitatively and quantitatively. All the Medical Imaging and Pattern Recognition algorithmic solutions studied for this Ph.D. Thesis have been integrated in GliCInE: Glioma Computerized Inspection Environment, which is a MATLAB prototype of an integrated analysis environment that offers, in addition to all the functionality specifically described in this Thesis, a set of tools needed to manage Functional and Structural Magnetic Resonance Volumes and ancillary data related to the acquisition and the patient.openInformaticaPedoia, ValentinaPedoia, Valentin

Towards development of automatic path planning system in image-guided neurosurgery

With the advent of advanced computer technology, many computer-aided systems have evolved to assist in medical related work including treatment, diagnosis, and even surgery. In modern neurosurgery, Magnetic Resonance Image guided stereotactic surgery exactly complies with this trend. It is a minimally invasive operation being much safer than the traditional open-skull surgery, and offers higher precision and more effective operating procedures compared to conventional craniotomy. However, such operations still face significant challenges of planning the optimal neurosurgical path in order to reach the ideal position without damage to important internal structures. This research aims to address this major challenge. The work begins with an investigation of the problem of distortion induced by MR images. It then goes on to build a template of the Circle of Wills brain vessels, realized from a collection of Magnetic Resonance Angiography images, which is needed to maintain operating standards when, as in many cases, Magnetic Resonance Angiography images are not available for patients. Demographic data of brain tumours are also studied to obtain further understanding of diseased human brains through the development of an effect classifier. The developed system allows the internal brain structure to be ‘seen’ clearly before the surgery, giving surgeons a clear picture and thereby makes a significant contribution to the eventual development of a fully automatic path planning system

An automated system for the classification and segmentation of brain tumours in MRI images based on the modified grey level co-occurrence matrix

The development of an automated system for the classification and segmentation of brain tumours in MRI scans remains challenging due to high variability and complexity of the brain tumours. Visual examination of MRI scans to diagnose brain tumours is the accepted standard. However due to the large number of MRI slices that are produced for each patient this is becoming a time consuming and slow process that is also prone to errors. This study explores an automated system for the classification and segmentation of brain tumours in MRI scans based on texture feature extraction. The research investigates an appropriate technique for feature extraction and development of a three-dimensional segmentation method. This was achieved by the investigation and integration of several image processing methods that are related to texture features and segmentation of MRI brain scans. First, the MRI brain scans were pre-processed by image enhancement, intensity normalization, background segmentation and correcting the mid-sagittal plane (MSP) of the brain for any possible skewness in the patient’s head. Second, the texture features were extracted using modified grey level co-occurrence matrix (MGLCM) from T2-weighted (T2-w) MRI slices and classified into normal and abnormal using multi-layer perceptron neural network (MLP). The texture feature extraction method starts from the standpoint that the human brain structure is approximately symmetric around the MSP of the brain. The extracted features measure the degree of symmetry between the left and right hemispheres of the brain, which are used to detect the abnormalities in the brain. This will enable clinicians to reject the MRI brain scans of the patients who have normal brain quickly and focusing on those who have pathological brain features. Finally, the bounding 3D-boxes based genetic algorithm (BBBGA) was used to identify the location of the brain tumour and segments it automatically by using three-dimensional active contour without edge (3DACWE) method. The research was validated using two datasets; a real dataset that was collected from the MRI Unit in Al-Kadhimiya Teaching Hospital in Iraq in 2014 and the standard benchmark multimodal brain tumour segmentation (BRATS 2013) dataset. The experimental results on both datasets proved that the efficacy of the proposed system in the successful classification and segmentation of the brain tumours in MRI scans. The achieved classification accuracies were 97.8% for the collected dataset and 98.6% for the standard dataset. While the segmentation’s Dice scores were 89% for the collected dataset and 89.3% for the standard dataset

Content based retrieval of PET neurological images

Medical image management has posed challenges to many researchers, especially when the images have to be indexed and retrieved using their visual content that is meaningful to clinicians. In this study, an image retrieval system has been developed for 3D brain PET (Position emission tomography) images. It has been found that PET neurological images can be retrieved based upon their diagnostic status using only data pertaining to their content, and predominantly the visual content. During the study PET scans are spatially normalized, using existing techniques, and their visual data is quantified. The mid-sagittal-plane of each individual 3D PET scan is found and then utilized in the detection of abnormal asymmetries, such as tumours or physical injuries. All the asymmetries detected are referenced to the Talairarch and Tournoux anatomical atlas. The Cartesian co- ordinates in Talairarch space, of detected lesion, are employed along with the associated anatomical structure(s) as the indices within the content based image retrieval system. The anatomical atlas is then also utilized to isolate distinct anatomical areas that are related to a number of neurodegenerative disorders. After segmentation of the anatomical regions of interest algorithms are applied to characterize the texture of brain intensity using Gabor filters and to elucidate the mean index ratio of activation levels. These measurements are combined to produce a single feature vector that is incorporated into the content based image retrieval system. Experimental results on images with known diagnoses show that physical lesions such as head injuries and tumours can be, to a certain extent, detected correctly. Images with correctly detected and measured lesion are then retrieved from the database of images when a query pertains to the measured locale. Images with neurodegenerative disorder patterns have been indexed and retrieved via texture-based features. Retrieval accuracy is increased, for images from patients diagnosed with dementia, by combining the texture feature and mean index ratio value

Content based retrieval of PET neurological images

Medical image management has posed challenges to many researchers, especially when the images have to be indexed and retrieved using their visual content that is meaningful to clinicians. In this study, an image retrieval system has been developed for 3D brain PET (Position emission tomography) images. It has been found that PET neurological images can be retrieved based upon their diagnostic status using only data pertaining to their content, and predominantly the visual content. During the study PET scans are spatially normalized, using existing techniques, and their visual data is quantified. The mid-sagittal-plane of each individual 3D PET scan is found and then utilized in the detection of abnormal asymmetries, such as tumours or physical injuries. All the asymmetries detected are referenced to the Talairarch and Tournoux anatomical atlas. The Cartesian co- ordinates in Talairarch space, of detected lesion, are employed along with the associated anatomical structure(s) as the indices within the content based image retrieval system. The anatomical atlas is then also utilized to isolate distinct anatomical areas that are related to a number of neurodegenerative disorders. After segmentation of the anatomical regions of interest algorithms are applied to characterize the texture of brain intensity using Gabor filters and to elucidate the mean index ratio of activation levels. These measurements are combined to produce a single feature vector that is incorporated into the content based image retrieval system. Experimental results on images with known diagnoses show that physical lesions such as head injuries and tumours can be, to a certain extent, detected correctly. Images with correctly detected and measured lesion are then retrieved from the database of images when a query pertains to the measured locale. Images with neurodegenerative disorder patterns have been indexed and retrieved via texture-based features. Retrieval accuracy is increased, for images from patients diagnosed with dementia, by combining the texture feature and mean index ratio value.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Automated morphometric analysis and phenotyping of mouse brains from structural µMR images

In light of the utility and increasing ubiquity of mouse models of genetic and neurological disease, I describefully automated pipelines for the investigation of structural microscopic magnetic resonance images of mouse brains – for both high-throughput phenotyping, and monitoring disease. Mouse models offer unparalleled insight into genetic function and brain plasticity, in phenotyping studies; and neurodegenerative disease onset and progression, in therapeutic trials. I developed two cohesive, automatic software tools, for Voxel- and Tensor-Based Morphometry (V/TBM) and the Boundary Shift Integral (BSI), in the mouse brain. V/TBM are advantageous for their ability to highlight morphological differences between groups, without laboriously delineating regions of interest. The BSI is a powerful and sensitive imaging biomarker for the detection of atrophy. The resulting pipelines are described in detail. I show the translation and application of open-source software developed for clinical MRI analysis to mouse brain data: for tissue segmentation into high-quality, subject-specific maps, using contemporary multi-atlas techniques; and for symmetric, inverse-consistent registration. I describe atlases and parameters suitable for the preclinical paradigm, and illustrate and discuss image processing challenges encountered and overcome during development. As proof of principle and to illustrate robustness, I used both pipelines with in and ex vivo mouse brain datasets to identify differences between groups, representing the morphological influence of genes, and subtle, longitudinal changes over time, in particular relation to Down syndrome and Alzheimer’s disease. I also discuss the merits of transitioning preclinical analysis from predominately ex vivo MRI to in vivo, where morphometry is still viable and fewer mice are necessary. This thesis conveys the cross-disciplinary translation of up-to-date image analysis techniques to the preclinical paradigm; the development of novel methods and adaptations to robustly process large cohorts of data; and the sensitive detection of phenotypic differences and neurodegenerative changes in the mouse brai