Automatic extraction of bronchus and centerline determination from CT images for three dimensional virtual bronchoscopy.

Law Tsui Ying.Thesis (M.Phil.)--Chinese University of Hong Kong, 2000.Includes bibliographical references (leaves 64-70).Abstracts in English and Chinese.Acknowledgments --- p.iiChapter 1 --- Introduction --- p.1Chapter 1.1 --- Structure of Bronchus --- p.3Chapter 1.2 --- Existing Systems --- p.4Chapter 1.2.1 --- Virtual Endoscope System (VES) --- p.4Chapter 1.2.2 --- Virtual Reality Surgical Simulator --- p.4Chapter 1.2.3 --- Automated Virtual Colonoscopy (AVC) --- p.5Chapter 1.2.4 --- QUICKSEE --- p.5Chapter 1.3 --- Organization of Thesis --- p.6Chapter 2 --- Three Dimensional Visualization in Medicine --- p.7Chapter 2.1 --- Acquisition --- p.8Chapter 2.1.1 --- Computed Tomography --- p.8Chapter 2.2 --- Resampling --- p.9Chapter 2.3 --- Segmentation and Classification --- p.9Chapter 2.3.1 --- Segmentation by Thresholding --- p.10Chapter 2.3.2 --- Segmentation by Texture Analysis --- p.10Chapter 2.3.3 --- Segmentation by Region Growing --- p.10Chapter 2.3.4 --- Segmentation by Edge Detection --- p.11Chapter 2.4 --- Rendering --- p.12Chapter 2.5 --- Display --- p.13Chapter 2.6 --- Hazards of Visualization --- p.13Chapter 2.6.1 --- Adding Visual Richness and Obscuring Important Detail --- p.14Chapter 2.6.2 --- Enhancing Details Incorrectly --- p.14Chapter 2.6.3 --- The Picture is not the Patient --- p.14Chapter 2.6.4 --- Pictures-'R'-Us --- p.14Chapter 3 --- Overview of Advanced Segmentation Methodologies --- p.15Chapter 3.1 --- Mathematical Morphology --- p.15Chapter 3.2 --- Recursive Region Search --- p.16Chapter 3.3 --- Active Region Models --- p.17Chapter 4 --- Overview of Centerline Methodologies --- p.18Chapter 4.1 --- Thinning Approach --- p.18Chapter 4.2 --- Volume Growing Approach --- p.21Chapter 4.3 --- Combination of Mathematical Morphology and Region Growing Schemes --- p.22Chapter 4.4 --- Simultaneous Borders Identification Approach --- p.23Chapter 4.5 --- Tracking Approach --- p.24Chapter 4.6 --- Distance Transform Approach --- p.25Chapter 5 --- Automated Extraction of Bronchus Area --- p.27Chapter 5.1 --- Basic Idea --- p.27Chapter 5.2 --- Outline of the Automated Extraction Algorithm --- p.28Chapter 5.2.1 --- Selection of a Start Point --- p.28Chapter 5.2.2 --- Three Dimensional Region Growing Method --- p.29Chapter 5.2.3 --- Optimization of the Threshold Value --- p.29Chapter 5.3 --- Retrieval of Start Point Algorithm Using Genetic Algorithm --- p.29Chapter 5.3.1 --- Introduction to Genetic Algorithm --- p.30Chapter 5.3.2 --- Problem Modeling --- p.31Chapter 5.3.3 --- Algorithm for Determining a Start Point --- p.33Chapter 5.3.4 --- Genetic Operators --- p.33Chapter 5.4 --- Three Dimensional Painting Algorithm --- p.34Chapter 5.4.1 --- Outline of the Three Dimensional Painting Algorithm --- p.34Chapter 5.5 --- Optimization of the Threshold Value --- p.36Chapter 6 --- Automatic Centerline Determination Algorithm --- p.38Chapter 6.1 --- Distance Transformations --- p.38Chapter 6.2 --- End Points Retrieval --- p.41Chapter 6.3 --- Graph Based Centerline Algorithm --- p.44Chapter 7 --- Experiments and Discussion --- p.48Chapter 7.1 --- Experiment of Automated Determination of Bronchus Algorithm --- p.48Chapter 7.2 --- Experiment of Automatic Centerline Determination Algorithm --- p.54Chapter 8 --- Conclusion --- p.62Bibliography --- p.6

Open-source virtual bronchoscopy for image guided navigation

This thesis describes the development of an open-source system for virtual bronchoscopy used in combination with electromagnetic instrument tracking. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. The open-source platform 3D Slicer was used for creating freely available algorithms for virtual bronchscopy. Firstly, the development of an open-source semi-automatic algorithm for prediction of solitary pulmonary nodule malignancy is presented. This approach may help the physician decide whether to proceed with biopsy of the nodule. The user-selected nodule is segmented in order to extract radiological characteristics (i.e., size, location, edge smoothness, calcification presence, cavity wall thickness) which are combined with patient information to calculate likelihood of malignancy. The overall accuracy of the algorithm is shown to be high compared to independent experts' assessment of malignancy. The algorithm is also compared with two different predictors, and our approach is shown to provide the best overall prediction accuracy. The development of an airway segmentation algorithm which extracts the airway tree from surrounding structures on chest Computed Tomography (CT) images is then described. This represents the first fundamental step toward the creation of a virtual bronchoscopy system. Clinical and ex-vivo images are used to evaluate performance of the algorithm. Different CT scan parameters are investigated and parameters for successful airway segmentation are optimized. Slice thickness is the most affecting parameter, while variation of reconstruction kernel and radiation dose is shown to be less critical. Airway segmentation is used to create a 3D rendered model of the airway tree for virtual navigation. Finally, the first open-source virtual bronchoscopy system was combined with electromagnetic tracking of the bronchoscope for the development of a GPS-like system for navigating within the lungs. Tools for pre-procedural planning and for helping with navigation are provided. Registration between the lungs of the patient and the virtually reconstructed airway tree is achieved using a landmark-based approach. In an attempt to reduce difficulties with registration errors, we also implemented a landmark-free registration method based on a balanced airway survey. In-vitro and in-vivo testing showed good accuracy for this registration approach. The centreline of the 3D airway model is extracted and used to compensate for possible registration errors. Tools are provided to select a target for biopsy on the patient CT image, and pathways from the trachea towards the selected targets are automatically created. The pathways guide the physician during navigation, while distance to target information is updated in real-time and presented to the user. During navigation, video from the bronchoscope is streamed and presented to the physician next to the 3D rendered image. The electromagnetic tracking is implemented with 5 DOF sensing that does not provide roll rotation information. An intensity-based image registration approach is implemented to rotate the virtual image according to the bronchoscope's rotations. The virtual bronchoscopy system is shown to be easy to use and accurate in replicating the clinical setting, as demonstrated in the pre-clinical environment of a breathing lung method. Animal studies were performed to evaluate the overall system performance

Effect of rib cage deformity in primary thoracic idiopathic scoliosis on pulmonary function, airway morphology and lung volumes

Although scoliosis is defined as a Cobb angle of 10° or more as measured in the coronal plane, the combined three-dimensional distortions to both the spine and rib cage in scoliosis are best conceptualised as a thoracic deformity. There is much interest in the relationship between scoliosis and pulmonary function due to the increased morbidity of respiratory failure and mortality of those with untreated progressive scoliosis. Establishing the mechanisms of pulmonary function impairment in scoliosis is important in identifying patients with compromised lung function or those who will benefit from surgical intervention. In this work, the relationship between thoracic deformity in patients with right-sided, Lenke type 1 or 2, adolescent idiopathic scoliosis (AIS) and pulmonary function impairment is investigated. From radiographic and computer tomographic imaging, measurements of the thoracic deformity were found to be superior predictors of pulmonary function in AIS than conventional Cobb angles. A statistical shape model was constructed from biplanar radiographs to identify modes of variation in the thoracic configuration. Thoracic features such as the extent of the rib hump, narrowed convex hemithoracic width and spinal intrusion were found to be factors contributing to lung function impairment. Morphological analysis of the tracheobronchial tree demonstrated the presence of right-sided airway narrowing. In particular, patients with hypokyphosis demonstrated significant narrowing of the bronchus intermedius and its bifurcation as a result of extrinsic compression by the vertebral column. Right-sided airway obstruction was found to correspond to the presence of atelectasis and air-trapping in the right middle and lower lobe. Post-operative analysis demonstrated that restoration of natural kyphosis in patients with hypokyphosis and scoliosis resulted in improved lung function post-operatively. Although reduction in lung function in patients with scoliosis is multifactorial, variance in the sagittal thoracic profile plays a more important role in impairing lung function than is generally appreciated

Automatic 3D extraction of pleural plaques and diffuse pleural thickening from lung MDCT images

Pleural plaques (PPs) and diffuse pleural thickening (DPT) are very common asbestos related pleural diseases (ARPD). They are currently identified non-invasively using medical imaging techniques. A fully automatic algorithm for 3D detection of calcified pleura in the diaphragmatic area and thickened pleura on the costal surfaces from multi detector computed tomography (MDCT) images has been developed and tested. The algorithm for detecting diaphragmatic pleura includes estimation of the diaphragm top surface in 3D and identifying those voxels at a certain vertical distance from the estimated diaphragm, and with intensities close to that of bone, as calcified pleura. The algorithm for detecting thickened pleura on the costal surfaces includes: estimation of the pleural costal surface in 3D, estimation of the centrelines of ribs and costal cartilages and the surfaces that they lie on, calculating the mean distance between the two surfaces, and identifying any space between the two surfaces whose distance exceeds the mean distance as thickened pleura. The accuracy and performance of the proposed algorithm was tested on 20 MDCT datasets from patients diagnosed with existing PPs and/or DPT and the results were compared against the ground truth provided by an experienced radiologist. Several metrics were employed and evaluations indicate high performance of both calcified pleura detection in the diaphragmatic area and thickened pleura on the costal surfaces. This work has made significant contributions to both medical image analysis and medicine. For the first time in medical image analysis, the approach uses other stable organs such as the ribs and costal cartilage, besides the lungs themselves, for referencing and landmarking in 3D. It also estimates fat thickness between the rib surface and pleura (which is usually very thin) and excludes it from the detected areas, when identifying the thickened pleura. It also distinguishes the calcified pleura attached to the rib(s), separates them in 3D and detects calcified pleura on the lung diaphragmatic surfaces. The key contribution to medicine is effective detection of pleural thickening of any size and recognition of any changes, however small. This could have a significant impact on managing patient risks

Interventional Bronchoscopy:State-of-the-Art Review

For over 150 years, bronchoscopy, especially flexible bronchoscopy, has been a mainstay for airway inspection, the diagnosis of airway lesions, therapeutic aspiration of airway secretions, and transbronchial biopsy to diagnose parenchymal lung disorders. Its utility for the diagnosis of peripheral pulmonary nodules and therapeutic treatments besides aspiration of airway secretions, however, has been limited. Challenges to the wider use of flexible bronchoscopy have included difficulty in navigating to the lung periphery, the avoidance of vasculature structures when performing diagnostic biopsies, and the ability to biopsy a lesion under direct visualization. The last 10-15 years have seen major advances in thoracic imaging, navigational platforms to direct the bronchoscopist to lung lesions, and the ability to visualize lesions during biopsy. Moreover, multiple new techniques have either become recently available or are currently being investigated to treat a broad range of airway and lung parenchymal diseases, such as asthma, emphysema, and chronic bronchitis, or to alleviate recurrent exacerbations. New bronchoscopic therapies are also being investigated to not only diagnose, but possibly treat, malignant peripheral lung nodules. As a result, flexible bronchoscopy is now able to provide a new and expanding armamentarium of diagnostic and therapeutic tools to treat patients with a variety of lung diseases. This State-of-the-Art review succinctly reviews these techniques and provides clinicians an organized approach to their role in the diagnosis and treatment of a range of lung diseases