Improved 3D thinning algorithms for skeleton extraction

In this study, we focused on developing a novel 3D Thinning algorithm to extract one-voxel wide skeleton from various 3D objects aiming at preserving the topological information. The 3D Thinning algorithm was testified on computer-generated and real 3D reconstructed image sets acquired from TEMT and compared with other existing 3D Thinning algorithms. It is found that the algorithm has conserved medial axes and simultaneously topologies very well, demonstrating many advantages over the existing technologies. They are versatile, rigorous, efficient and rotation invariant.<br /

CAD MODEL OF PATIENT SPECIFIC PORTAL VEIN FOR ANALYSIS OF LIVER DISORDER

Recent days Computer-aided design and image processing techniques are one of the most emerging useful tools for analysis of models in various medical, industrial and research areas. In medical field for the diagnosis of various diseases in vivo techniques including biochemical test, enzymatic tests are needed for continuous monitoring of patients. These diagnosis procedures are time consuming and inconvenient for patients. Therefore Computer assisted designing and image processing techniques are most promising non invasive tools for faster diagnosis and useful tool for designing of biomedical implants. In this paper portal vein was segmented from patient’s Liver computed tomography (CT) image by dedicated software. A Liver’s CT image of 38 year old Indian male patient’s was collected and by using imaged based software MIMICS (Materialise’s Interactive Medical Image Control System, Belgium) 3D model of HPV (hepatic portal vein) was obtained and Solid Work Professional (Dassault Systems Solid Works Corporation, USA) software was used for designing of normal portal vein’s 3D model and various portal vein diseased models including minor right portal vein thrombosis ( 19- 20% reduction in medial region of vein), severe right portal vein thrombosis (20-22% reduction in medial and distal region of vein), minor left portal vein thrombosis (19-20% reduction in medial region of vein, severe right portal vein thrombosis(20-22% reduction in medial and distal region of vein), left aneurysm (150-200 % increase of medial region).These models can be used for designing for implants and analysis of portal vein’s disorder like portal thrombosis, and portal aneurysm which are main cause of portal hypertension and also useful for surgeon for planning surgery and also helpful for understanding of portal vein hemodynamic (pressure, velocity, wall shear force

Spectrum skeletonization : a new method for acoustic signal extraction

Vibration Analysis Tests (VAT) and Acoustic Emission tests (AE) are used in several industrial applications. Many of them perform analysis in the frequency domain. Peaks in the power density spectrum hold relevant information about acoustic events. In this paper we propose a novel method for feature extraction of vibration samples by analyzing the shape of their auto power spectrum density function. The approach uses skeletonization techniques in order to find the hierarchical structure of the spectral peaks. The proposed method can be applied as a preprocessing step for spectrum analysis of vibration signals

Automated airway quantification associates with mortality in idiopathic pulmonary fibrosis

OBJECTIVES: The study examined whether quantified airway metrics associate with mortality in idiopathic pulmonary fibrosis (IPF). METHODS: In an observational cohort study (n = 90) of IPF patients from Ege University Hospital, an airway analysis tool AirQuant calculated median airway intersegmental tapering and segmental tortuosity across the 2nd to 6th airway generations. Intersegmental tapering measures the difference in median diameter between adjacent airway segments. Tortuosity evaluates the ratio of measured segmental length against direct end-to-end segmental length. Univariable linear regression analyses examined relationships between AirQuant variables, clinical variables, and lung function tests. Univariable and multivariable Cox proportional hazards models estimated mortality risk with the latter adjusted for patient age, gender, smoking status, antifibrotic use, CT usual interstitial pneumonia (UIP) pattern, and either forced vital capacity (FVC) or diffusion capacity of carbon monoxide (DLco) if obtained within 3 months of the CT. RESULTS: No significant collinearity existed between AirQuant variables and clinical or functional variables. On univariable Cox analyses, male gender, smoking history, no antifibrotic use, reduced DLco, reduced intersegmental tapering, and increased segmental tortuosity associated with increased risk of death. On multivariable Cox analyses (adjusted using FVC), intersegmental tapering (hazard ratio (HR) = 0.75, 95% CI = 0.66-0.85, p < 0.001) and segmental tortuosity (HR = 1.74, 95% CI = 1.22-2.47, p = 0.002) independently associated with mortality. Results were maintained with adjustment using DLco. CONCLUSIONS: AirQuant generated measures of intersegmental tapering and segmental tortuosity independently associate with mortality in IPF patients. Abnormalities in proximal airway generations, which are not typically considered to be abnormal in IPF, have prognostic value. CLINICAL RELEVANCE STATEMENT: Quantitative measurements of intersegmental tapering and segmental tortuosity, in proximal (second to sixth) generation airway segments, independently associate with mortality in IPF. Automated airway analysis can estimate disease severity, which in IPF is not restricted to the distal airway tree. KEY POINTS: • AirQuant generates measures of intersegmental tapering and segmental tortuosity. • Automated airway quantification associates with mortality in IPF independent of established measures of disease severity. • Automated airway analysis could be used to refine patient selection for therapeutic trials in IPF

Novel CT-based objective imaging biomarkers of long term radiation-induced lung damage

Background: and Purpose: Recent improvements in lung cancer survival have spurred an interest in understanding and minimizing long term radiation-induced lung damage (RILD). However, there is still no objective criteria to quantify RILD leading to variable reporting across centres and trials. We propose a set of objective imaging biomarkers to quantify common radiological findings observed 12-months after lung cancer radiotherapy (RT). Material and Methods: Baseline and 12-month CT scans of 27 patients from a phase I/II clinical trial of isotoxic chemoradiation were included in this study. To detect and measure the severity of RILD, twelve quantitative imaging biomarkers were developed. These describe basic CT findings including parenchymal change, volume reduction and pleural change. The imaging biomarkers were implemented as semi-automated image analysis pipelines and assessed against visual assessment of the occurrence of each change. Results: The majority of the biomarkers were measurable in each patient. Their continuous nature allows objective scoring of severity for each patient. For each imaging biomarker the cohort was split into two groups according to the presence or absence of the biomarker by visual assessment, testing the hypothesis that the imaging biomarkers were different in these two groups. All features were statistically significant except for rotation of the main bronchus and diaphragmatic curvature. The majority of the biomarkers were not strongly correlated with each other suggesting that each of the biomarkers is measuring a separate element of RILD pathology. Conclusions: We developed objective CT-based imaging biomarkers that quantify the severity of radiological lung damage after RT. These biomarkers are representative of typical radiological findings of RILD

Automated Neurovascular Tracing and Analysis of the Knife-Edge Scanning Microscope India Ink Data Set

The 3D reconstruction of neurovascular network plays an important role in understanding the functions of the blood vessels in different brain regions. Many techniques have been applied to acquire microscopic neurovascular data. The Knife-Edge Scanning Microscope (KESM) is a physical sectioning microscopy instrument developed by the Brain Network Lab in Texas A&M University which enables imaging of an entire mouse brain at sub-micrometer resolution. With the KESM image data, we can trace the neurovascular structure of the whole mouse brain. For the large neurovascular volume like the KESM data set, complicated tracing algorithm with template matching process is not fast enough. Also, KESM imaging might involve gaps and noise in data when acquiring the large volume of data. To solve these issues, a novel automated neurovascular tracing and data analysis method with less processing time and high accuracy is developed in this thesis. First, an automated seed point selection algorithm was described in my approach. The seed points on every outer boundary surface of the volume were selected as the start points of tracing. Second, a vector-based tracing method was developed to trace vascular network in 3D space. Third, the properties of the extracted vascular network were analyzed. Finally, the accuracy of the tracing method was evaluated using synthetic data. This approach is expected to help explore the entire vascular network of KESM automatically without human assistance

Knife Edge Scanning Microscope Brain Atlas Interface for Tracing and Analysis of Vasculature Data

The study of the neurovascular network in the brain is important to understand brain functions as well as causes of several brain dysfunctions. Many techniques have been applied to acquire neurovascular data. The Knife-Edge Scanning Microscope (KESM), developed by the Brain Network Lab at Texas A&M University, can generate whole-brain-scale data at submicrometer resolution. The specimen can be stained with different stains, and depending on the type of stain used, the KESM can image different types of microstructures in the brain. The India ink stain allows the neurovascular network in the brain to be imaged. In order to visualize and analyze such large datasets (~ 1.5 TB per brain), a lightweight, web-based mouse brain atlas called the Knife-Edge Scanning Microscope Brain Atlas (KESMBA) was developed in the lab. The atlas serves several whole mouse brain data sets including India ink. The multi-section overlay technique used in the atlas enables 3D visualization of the structural information in the data. To solve the challenging issue of tracing micro-vessels in the brain, in this thesis a semi-automated tracing and analysis method is developed and integrated into the KESM brain atlas. Using the KESMBA interface developed in this thesis, the user can look at the 3D structure of the vessels on the brain atlas and can guide the tracing algorithm. To analyze the vasculature network traced by the user, a data analysis component is also added. This new KESMBA interface is expected to help in quickly tracing and analyzing the vascular network of the brain with minimal manual effort. In order to visualize and analyze such large data sets (~ 1.5 TB per brain), a light-weight, web-based mouse brain atlas called the Knife-Edge Scanning Microscope Brain Atlas (KESMBA) was developed in the lab. The atlas serves several whole mouse brain data sets including India ink. The multi-section overlay technique used in the atlas enables 3D visualization of the structural information in the data. To solve the challenging issue of tracing micro-vessels in the brain, in this thesis a semi-automated tracing and analysis method is developed and integrated into the KESM brain atlas. Using the KESMBA interface developed in this thesis, the user can look at the 3D structure of the vessels on the brain atlas and can guide the tracing algorithm. In order to analyze the vasculature network traced by the user, a data analysis component is also added. This new KESMBA interface is expected to help in quickly tracing and analyzing the vascular network of the brain with minimal manual effort

L-systems from 3D-imaging of phenotypes of arborized structures

Biology is 3D. Therefore, it is important to be able to analyze phenomena in a spatiotemporal manner. Different fields in computational sciences are useful for analysis in biology; i.e. image analysis, pattern recognition and machine learning. To fit an empirical model to a higher abstraction, however, theoretical computer science methods are probed. We explore the construction of empirical 3D graphical models and develop abstractions from these models in L-systems. These systems are provided with a profound formalization in a grammar allowing generalization and exploration of mathematical structures in topologies. The connections between these computational approaches are illustrated by a case study of the development of the lactiferous duct in mice and the phenotypical effects from different environmental conditions we can observe on it. We have constructed a workflow to get 3D models from different experimental conditions and use these models to extract features. Our aim is to construct an abstraction of these 3D models to an L-system from features that we have measured. From our measurements we can make the productions for an L-system. In this manner we can formalize the arborization of the lactiferous duct under different environmental conditions and capture different observations. All considered, this paper illustrates the joint of empirical with theoretical computational sciences and the augmentation of the interpretation of the results. At the same time, it shows a method to analyze complex 3D topologies and produces archetypes for developmental configurations.Algorithms and the Foundations of Software technolog