Image and Volume Segmentation by Water Flow

A general framework for image segmentation is presented in this paper, based on the paradigm of water flow. The major water flow attributes like water pressure, surface tension and capillary force are defined in the context of force field generation and make the model adaptable to topological and geometrical changes. A flow-stopping image functional combining edge- and region-based forces is introduced to produce capability for both range and accuracy. The method is assessed qualitatively and quantitatively on synthetic and natural images. It is shown that the new approach can segment objects with complex shapes or weak-contrasted boundaries, and has good immunity to noise. The operator is also extended to 3-D, and is successfully applied to medical volume segmentation

3D vasculature segmentation using localized hybrid level-set method

Background: Intensity inhomogeneity occurs in many medical images, especially in vessel images. Overcoming the difficulty due to image inhomogeneity is crucial for the segmentation of vessel image. Methods: This paper proposes a localized hybrid level-set method for the segmentation of 3D vessel image. The proposed method integrates both local region information and boundary information for vessel segmentation, which is essential for the accurate extraction of tiny vessel structures. The local intensity information is firstly embedded into a region-based contour model, and then incorporated into the level-set formulation of the geodesic active contour model. Compared with the preset global threshold based method, the use of automatically calculated local thresholds enables the extraction of the local image information, which is essential for the segmentation of vessel images. Results: Experiments carried out on the segmentation of 3D vessel images demonstrate the strengths of using locally specified dynamic thresholds in our level-set method. Furthermore, both qualitative comparison and quantitative validations have been performed to evaluate the effectiveness of our proposed model. Conclusions: Experimental results and validations demonstrate that our proposed model can achieve more promising segmentation results than the original hybrid method does

Robust semi-automated path extraction for visualising stenosis of the coronary arteries

Computed tomography angiography (CTA) is useful for diagnosing and planning treatment of heart disease. However, contrast agent in surrounding structures (such as the aorta and left ventricle) makes 3-D visualisation of the coronary arteries difficult. This paper presents a composite method employing segmentation and volume rendering to overcome this issue. A key contribution is a novel Fast Marching minimal path cost function for vessel centreline extraction. The resultant centreline is used to compute a measure of vessel lumen, which indicates the degree of stenosis (narrowing of a vessel). Two volume visualisation techniques are presented which utilise the segmented arteries and lumen measure. The system is evaluated and demonstrated using synthetic and clinically obtained datasets

Compression of 4D medical image and spatial segmentation using deformable models

Ph.DDOCTOR OF PHILOSOPH

Brain vasculature segmentation from magnetic resonance angiographic image

Master'sMASTER OF ENGINEERIN

Computational methods to predict and enhance decision-making with biomedical data.

The proposed research applies machine learning techniques to healthcare applications. The core ideas were using intelligent techniques to find automatic methods to analyze healthcare applications. Different classification and feature extraction techniques on various clinical datasets are applied. The datasets include: brain MR images, breathing curves from vessels around tumor cells during in time, breathing curves extracted from patients with successful or rejected lung transplants, and lung cancer patients diagnosed in US from in 2004-2009 extracted from SEER database. The novel idea on brain MR images segmentation is to develop a multi-scale technique to segment blood vessel tissues from similar tissues in the brain. By analyzing the vascularization of the cancer tissue during time and the behavior of vessels (arteries and veins provided in time), a new feature extraction technique developed and classification techniques was used to rank the vascularization of each tumor type. Lung transplantation is a critical surgery for which predicting the acceptance or rejection of the transplant would be very important. A review of classification techniques on the SEER database was developed to analyze the survival rates of lung cancer patients, and the best feature vector that can be used to predict the most similar patients are analyzed

Multi-parametric quantitative microvascular imaging with optical-resolution photoacoustic microscopy in vivo

Many diseases involve either the formation of new blood vessels (e.g., tumor angiogenesis) or the damage of existing ones (e.g., diabetic retinopathy) at the microcirculation level. Optical-resolution photoacoustic microscopy (OR-PAM), capable of imaging microvessels in 3D in vivo down to individual capillaries using endogenous contrast, has the potential to reveal microvascular information critical to the diagnosis and staging of microcirculation-related diseases. In this study, we have developed a dedicated microvascular quantification (MQ) algorithm for OR-PAM to automatically quantify multiple microvascular morphological parameters in parallel, including the vessel diameter distribution, the microvessel density, the vascular tortuosity, and the fractal dimension. The algorithm has been tested on in vivo OR-PAM images of a healthy mouse, demonstrating high accuracy for microvascular segmentation and quantification. The developed MQ algorithm for OR-PAM may greatly facilitate quantitative imaging of tumor angiogenesis and many other microcirculation related diseases in vivo

Accurate geometry reconstruction of vascular structures using implicit splines

3-D visualization of blood vessel from standard medical datasets (e.g. CT or MRI) play an important role in many clinical situations, including the diagnosis of vessel stenosis, virtual angioscopy, vascular surgery planning and computer aided vascular surgery. However, unlike other human organs, the vasculature system is a very complex network of vessel, which makes it a very challenging task to perform its 3-D visualization. Conventional techniques of medical volume data visualization are in general not well-suited for the above-mentioned tasks. This problem can be solved by reconstructing vascular geometry. Although various methods have been proposed for reconstructing vascular structures, most of these approaches are model-based, and are usually too ideal to correctly represent the actual variation presented by the cross-sections of a vascular structure. In addition, the underlying shape is usually expressed as polygonal meshes or in parametric forms, which is very inconvenient for implementing ramification of branching. As a result, the reconstructed geometries are not suitable for computer aided diagnosis and computer guided minimally invasive vascular surgery. In this research, we develop a set of techniques associated with the geometry reconstruction of vasculatures, including segmentation, modelling, reconstruction, exploration and rendering of vascular structures. The reconstructed geometry can not only help to greatly enhance the visual quality of 3-D vascular structures, but also provide an actual geometric representation of vasculatures, which can provide various benefits. The key findings of this research are as follows: 1. A localized hybrid level-set method of segmentation has been developed to extract the vascular structures from 3-D medical datasets. 2. A skeleton-based implicit modelling technique has been proposed and applied to the reconstruction of vasculatures, which can achieve an accurate geometric reconstruction of the vascular structures as implicit surfaces in an analytical form. 3. An accelerating technique using modern GPU (Graphics Processing Unit) is devised and applied to rendering the implicitly represented vasculatures. 4. The implicitly modelled vasculature is investigated for the application of virtual angioscopy

Deep Learning for Vascular Segmentation and Applications in Phase Contrast Tomography Imaging

Automated blood vessel segmentation is vital for biomedical imaging, as vessel changes indicate many pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. We present a thorough literature review, highlighting the state of machine learning techniques across diverse organs. Our goal is to provide a foundation on the topic and identify a robust baseline model for application to vascular segmentation in a new imaging modality, Hierarchical Phase Contrast Tomography (HiP CT). Introduced in 2020 at the European Synchrotron Radiation Facility, HiP CT enables 3D imaging of complete organs at an unprecedented resolution of ca. 20mm per voxel, with the capability for localized zooms in selected regions down to 1mm per voxel without sectioning. We have created a training dataset with double annotator validated vascular data from three kidneys imaged with HiP CT in the context of the Human Organ Atlas Project. Finally, utilising the nnU Net model, we conduct experiments to assess the models performance on both familiar and unseen samples, employing vessel specific metrics. Our results show that while segmentations yielded reasonably high scores such as clDice values ranging from 0.82 to 0.88, certain errors persisted. Large vessels that collapsed due to the lack of hydrostatic pressure (HiP CT is an ex vivo technique) were segmented poorly. Moreover, decreased connectivity in finer vessels and higher segmentation errors at vessel boundaries were observed. Such errors obstruct the understanding of the structures by interrupting vascular tree connectivity. Through our review and outputs, we aim to set a benchmark for subsequent model evaluations using various modalities, especially with the HiP CT imaging database