Automatic pulmonary fissure detection and lobe segmentation in CT chest images.

BACKGROUND: Multi-detector Computed Tomography has become an invaluable tool for the diagnosis of chronic respiratory diseases. Based on CT images, the automatic algorithm to detect the fissures and divide the lung into five lobes will help regionally quantify, amongst others, the lung density, texture, airway and, blood vessel structures, ventilation and perfusion. METHODS: Sagittal adaptive fissure scanning based on the sparseness of the vessels and bronchi is employed to localize the potential fissure region. Following a Hessian matrix based line enhancement filter in the coronal slice, the shortest path is determined by means of Uniform Cost Search. Implicit surface fitting based on Radial Basis Functions is used to extract the fissure surface for lobe segmentation. By three implicit fissure surface functions, the lung is divided into five lobes. The proposed algorithm is tested by 14 datasets. The accuracy is evaluated by the mean (±S.D.), root mean square, and the maximum of the shortest Euclidian distance from the manually-defined fissure surface to that extracted by the algorithm. RESULTS: Averaged over all datasets, the mean (±S.D.), root mean square, and the maximum of the shortest Euclidian distance are 2.05 ± 1.80, 2.46 and 7.34 mm for the right oblique fissure. The measures are 2.77 ± 2.12, 3.13 and 7.75 mm for the right horizontal fissure, 2.31 ± 1.76, 3.25 and 6.83 mm for the left oblique fissure. The fissure detection works for the data with a small lung nodule nearby the fissure and a small lung subpleural nodule. The volume and emphysema index of each lobe can be calculated. The algorithm is very fast, e.g., to finish the fissure detection and fissure extension for the dataset with 320 slices only takes around 50 seconds. CONCLUSIONS: The sagittal adaptive fissure scanning can localize the potential fissure regions quickly. After the potential region is enhanced by a Hessian based line enhancement filter, Uniform Cost Search can extract the fissures successfully in 2D. Surface fitting is able to obtain three implicit surface functions for each dataset. The current algorithm shows good accuracy, robustness and speed, may help locate the lesions into each lobe and analyze them regionally.

Computational fluid dynamics simulation of airflow in the trachea and main bronchi for the subjects with left pulmonary artery sling.

BACKGROUND: Left pulmonary artery sling (LPAS) is a rare but severe congenital anomaly, in which the stenoses are formed in the trachea and/or main bronchi. Multi-detector computed tomography (MDCT) provides useful anatomical images, but does not offer functional information. The objective of the present study is to quantitatively analyze the airflow in the trachea and main bronchi of LPAS subjects through computational fluid dynamics (CFD) simulation. METHODS: Five subjects (four LPAS patients, one normal control) aging 6-19 months are analyzed. The geometric model of the trachea and the two main bronchi is extracted from the MDCT images. The inlet velocity is determined based on the body weight and the inlet area. Both the geometric model and personalized inflow conditions are imported into CFD software, ANSYS. The pressure drop, mass flow ratio through two bronchi, wall pressure, flow velocity and wall shear stress (WSS) are obtained, and compared to the normal control. RESULTS: Due to the tracheal and/or bronchial stenosis, the pressure drop for the LPAS patients ranges 78.9-914.5 Pa, much higher than for the normal control (0.7 Pa). The mass flow ratio through the two bronchi does not correlate with the sectional area ratio if the anomalous left pulmonary artery compresses the trachea or bronchi. It is suggested that the C-shaped trachea plays an important role on facilitating the air flow into the left bronchus with the inertia force. For LPAS subjects, the distributions of velocities, wall pressure and WSS are less regular than for the normal control. At the stenotic site, high velocity, low wall pressure and high WSS are observed. CONCLUSIONS: Using geometric models extracted from CT images and the patient-specified inlet boundary conditions, CFD simulation can provide vital quantitative flow information for LPAS. Due to the stenosis, high pressure drops, inconsistent distributions of velocities, wall pressure and WSS are observed. The C-shaped trachea may facilitate a larger flow of air into the left bronchus under the inertial force, and decrease the ventilation of the right lung. Quantitative and personalized information may help understand the mechanism of LPAS and the correlations between stenosis and dyspnea, and facilitate the structural and functional assessment of LPAS.

Automatic segmentation of juxta-pleural tumors from CT images based on morphological feature analysis.

Extraction of lung tumors is a fundamental step for further quantitative analysis of the tumor, but is challenging for juxta-pleural tumors due to the adhesion to the pleurae. An automatic algorithm for segmentation of juxta-pleural tumors based on the analysis of the geometric and morphological features was proposed. Initially, the lung is extracted by means of thresholding using 2D Otsu's method. Next a center point is suggested to find a starting point and endpoint of outward facing pleura. A model based on the variation of incline angle was adopted to identify potentially affected regions, and to full segment juxta-pleural tumors. The results were compared with the manual segmentation by two radiologists. Averaged for ten experimental datasets, the accuracy calculated by Dice index between the results of the algorithm and by the two radiologists is 91.2%. It indicates the proposed method has comparable accuracy with the experts (the inter-observer variability is 92.4%), but requests much less manual interactions. The proposed algorithm can be used for segmenting juxta-pleural tumors from CT images, and help improve the diagnosis, pre-operative planning and therapy response evaluation.

PhenOMIM: an OMIM-based secondary database purported for phenotypic comparison.

Phenotypic comparison may provide crucial information for obtaining insights into molecular interactions underlying various diseases. However, few attempts have been made to systematically analyze the phenotypes of hereditary disorders, mainly owing to the poor quality of text descriptions and lack of a unified system of descriptors. Here we present a secondary database, PHENOMIM, for translating the phenotypic data obtained from the Online Mendelian Inheritance in Man (OMIM) database into a structured form. Moreover, a web interface has also been developed for visualizing the data and related information from the OMIM and PhenOMIM databases. The data is freely available online for reviewing and commenting purposes and can be found at http://faculty.neu.edu.cn/bmie/han/PhenOMIM/.

Arterial radius estimation from microscopic data using a new algorithm for circle parameter estimation.

We develop and test a new method for automatic determination of vessel wall diameters from image stacks obtained using two-photon laser scanning microscopy (TPLSM) on viable arteries in perfusion flow chambers. To this extent, a new method is proposed for estimating the parameters of a circle describing the inner diameter of the blood vessels. The new method is based on the Hough transform and the observation that three points that are not colinear uniquely define a circle. By only storing the estimated center location, the computational and memory costs of the Hough transform can be greatly reduced. We test the algorithm on 20 images and compare the result with a ground-truth established by human volunteers and a standard least-squares technique. With errors of 3 to 5%, the algorithm enables accurate estimation of the vessel diameters from image stacks containing only small parts of the vessel cross section. Combined with TPLSM imaging of anatomical vessel wall properties, potentially, the algorithm enables the correlation of structural and functional properties of large intact arteries simultaneously, without requirements for additional experiments.