Three-dimensional segmentation and skeletonization to build an airway tree data structure for small animals

Abstract

Quantitative analysis of intrathoracic airway tree geometry is important for objective evaluation of bronchial tree structure and function. Currently, there is more human data than small animal data on airway morphometry. In this study, we implemented a semi-automatic approach to quantitatively describe airway tree geometry by using high-resolution computed tomography (CT) images to build a tree data structure for small animals such as rats and mice. Silicon lung casts of the excised lungs from a canine and a mouse were used for micro-CT imaging of the airway trees. The programming language IDL was used to implement a 3D region-growing threshold algorithm for segmenting out the airway lung volume from the CT data. Subsequently, a fully-parallel 3D thinning algorithm was implemented in order to complete the skeletonization of the segmented airways. A tree data structure was then created and saved by parsing through the skeletonized volume using the Python programming language. Pertinent information such as the length of all airway segments was stored in the data structure. This approach was shown to be accurate and efficient for up to six generations for the canine lung cast and ten generations for the mouse lung cast.

Building Human Brain Network in 3D Coefficient Map Determined by X-ray Microtomography

“…Structural analyses of tomographic images based on model building have been reported for a number of organs, e.g., pulmonary airway [11] and intervertebral disc [12]. Our results indicate that model building in the microtomographic image at cellular to subcellular resolution can reveal the mechanisms of biological functions.…”

Lung structure phenotype variation in inbred mouse strains revealed through in vivo micro-CT imaging

“…However, to date, no comparison of the size and shape of the airways in these mice in vivo has been completed. Studies evaluating the morphology of the airway structures in the mouse have used lung casting techniques where manual caliper measurements of airway length, diameter, and branching angle have been made (4,17). More recently, micro-CT imaging of these airway casts has also been completed for a more rigorous quantitative analysis and development of an airway tree data structure (4).…”

Study of the Variability in Upper and Lower Airway Morphology in Sprague–Dawley Rats Using Modern Micro‐CT Scan‐Based Segmentation Techniques

“…Advances in small animal imaging using micro-CT or MRI have made it possible to study the respiratory system in a specific animal into great detail (Johnson, 2007;Lam et al, 2007;Wietholt et al, 2008). Earlier work by Chaturvedi and Lee (Chaturvedi and Lee, 2005) has used micro CT images to accurately study the morphology of the mouse and canine airway tract based on lung casts and segmentation principles. The study we present here uses similar techniques but scans are performed in vivo or in situ.…”