Segmentation of Tubular Structures Using Iterative Training with Tailored Samples

We propose a minimal path method to simultaneously compute segmentation masks and extract centerlines of tubular structures with line-topology. Minimal path methods are commonly used for the segmentation of tubular structures in a wide variety of applications. Recent methods use features extracted by CNNs, and often outperform methods using hand-tuned features. However, for CNN-based methods, the samples used for training may be generated inappropriately, so that they can be very different from samples encountered during inference. We approach this discrepancy by introducing a novel iterative training scheme, which enables generating better training samples specifically tailored for the minimal path methods without changing existing annotations. In our method, segmentation masks and centerlines are not determined after one another by post-processing, but obtained using the same steps. Our method requires only very few annotated training images. Comparison with seven previous approaches on three public datasets, including satellite images and medical images, shows that our method achieves state-of-the-art results both for segmentation masks and centerlines.Comment: Accepted to IEEE/CVF International Conference on Computer Vision (ICCV), Paris, 202

A graph-based mathematical morphology reader

This survey paper aims at providing a "literary" anthology of mathematical morphology on graphs. It describes in the English language many ideas stemming from a large number of different papers, hence providing a unified view of an active and diverse field of research

Minimal Path Methods for Segmentation and Analysis of 2D and 3D Line Structures

Image segmentation plays a vital role in many applications of computer vision. Segmentation is not only an important task in its own right, but also a prerequisite for many further image analysis steps. Consequently, segmentation is one of the most active research areas of computer vision. In this thesis, line structures are considered, which have quite different characteristics compared to common objects in natural 2D images: Line structures are much thinner and longer, and often they have little color or texture information such as blood vessels in medical images. To cope with these challenges, minimal path methods are commonly used. In this thesis, two new methods are introduced which are extensions of existing minimal path methods. The first method is a novel hybrid approach for automatic 3D segmentation and quantification of high-resolution 7 Tesla magnetic resonance angiography (MRA) images of the human cerebral vasculature. Our approach consists of two main steps. First, a 3D model-based approach is used to segment and quantify thick vessels and most parts of thin vessels. Second, remaining vessel gaps of the first step in low-contrast and noisy regions are completed using a 3D minimal path approach, which exploits directional information. We present two novel minimal path approaches: The first is an explicit approach based on energy minimization using probabilistic sampling, and the second is an implicit approach based on fast marching with anisotropic directional prior. The second method we introduce is a novel minimal path method for the segmentation of 2D and 3D line structures. Minimal path methods perform propagation of a wavefront emanating from a start point at a speed derived from image features, followed by path extraction using backtracing. Usually, the computation of the speed and the propagation of the wave are two separate steps, and point features are used to compute a static speed. We introduce a new continuous minimal path method which steers the wave propagation progressively using dynamic speed based on path features. We present three instances of our method, using an appearance feature of the path, a geometric feature based on the curvature of the path, and a joint appearance and geometric feature based on the tangent of the wavefront. Such features have not been used in previous continuous minimal path methods. We compute the features dynamically during the wave propagation, and also efficiently using a fast numerical scheme and a low-dimensional parameter space. Our method does not suffer from discretization or metrication errors. We conducted quantitative and qualitative experimental evaluations of our methods using 2D and 3D images from different application areas, including synthetic images, retinal images, satellite images of streets, rivers, and bridges, and 3D 7T MRA images of human brain vessels

Dimensional Changes of Upper Airway after Rapid Maxillary Expansion: A Prospective Cone-beam Computed Tomography Study

Introduction: The aim of this prospective study was to use cone-beam computed tomography to assess the dimensional changes of the upper airway in orthodontic patients with maxillary constriction treated by rapid maxillary expansion. Methods: Fourteen orthodontic patients (mean age, 12.9 years; range, 9.7-16 years) were recruited. The patients with posterior crossbite and constricted maxilla were treated with rapid maxillary expansion as the initial part of their comprehensive orthodontic treatments. Before and after rapid maxillary expansion conebeam computed tomography scans were taken to measure the retropalatal and retroglossal airway changes in terms of volume, and sagittal and cross-sectional areas. The transverse expansions by rapid maxillary expansion were assessed between the midlingual alveolar bone plates at the maxillary first molar and first premolar levels. The measurements of the before and after rapid maxillary expansion scans were compared by using paired t tests with the Bonferroni adjustment for multiple comparisons. Results: After rapid maxillary expansion, significant and equal amounts of 4.8 mm of expansion were observed at the first molar (P 5 0.0000) and the first premolar (P 5 0.0000) levels. The width increase at the first premolar level (20.0%) was significantly greater than that at the first molar level (15.0%) (P 5 0.035). As the primary outcome variable, the cross-sectional airway measured from the posterior nasal spine to basion level was the only parameter showing a significant increase of 99.4 mm2 (59.6%) after rapid maxillary expansion (P 5 0.0004). Conclusions: These results confirm the findings of previous studies of the effect of rapid maxillary expansion on the maxilla. Additionally, we found that only the cross-sectional area of the upper airway at the posterior nasal spine to basion level significantly gains a moderate increase after rapid maxillary expansion

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Coronary Artery Segmentation and Motion Modelling

Conventional coronary artery bypass surgery requires invasive sternotomy and the use of a cardiopulmonary bypass, which leads to long recovery period and has high infectious potential. Totally endoscopic coronary artery bypass (TECAB) surgery based on image guided robotic surgical approaches have been developed to allow the clinicians to conduct the bypass surgery off-pump with only three pin holes incisions in the chest cavity, through which two robotic arms and one stereo endoscopic camera are inserted. However, the restricted field of view of the stereo endoscopic images leads to possible vessel misidentification and coronary artery mis-localization. This results in 20-30% conversion rates from TECAB surgery to the conventional approach. We have constructed patient-specific 3D + time coronary artery and left ventricle motion models from preoperative 4D Computed Tomography Angiography (CTA) scans. Through temporally and spatially aligning this model with the intraoperative endoscopic views of the patient's beating heart, this work assists the surgeon to identify and locate the correct coronaries during the TECAB precedures. Thus this work has the prospect of reducing the conversion rate from TECAB to conventional coronary bypass procedures. This thesis mainly focus on designing segmentation and motion tracking methods of the coronary arteries in order to build pre-operative patient-specific motion models. Various vessel centreline extraction and lumen segmentation algorithms are presented, including intensity based approaches, geometric model matching method and morphology-based method. A probabilistic atlas of the coronary arteries is formed from a group of subjects to facilitate the vascular segmentation and registration procedures. Non-rigid registration framework based on a free-form deformation model and multi-level multi-channel large deformation diffeomorphic metric mapping are proposed to track the coronary motion. The methods are applied to 4D CTA images acquired from various groups of patients and quantitatively evaluated

Vid2Curve: Simultaneous Camera Motion Estimation and Thin Structure Reconstruction from an RGB Video

Thin structures, such as wire-frame sculptures, fences, cables, power lines, and tree branches, are common in the real world. It is extremely challenging to acquire their 3D digital models using traditional image-based or depth-based reconstruction methods because thin structures often lack distinct point features and have severe self-occlusion. We propose the first approach that simultaneously estimates camera motion and reconstructs the geometry of complex 3D thin structures in high quality from a color video captured by a handheld camera. Specifically, we present a new curve-based approach to estimate accurate camera poses by establishing correspondences between featureless thin objects in the foreground in consecutive video frames, without requiring visual texture in the background scene to lock on. Enabled by this effective curve-based camera pose estimation strategy, we develop an iterative optimization method with tailored measures on geometry, topology as well as self-occlusion handling for reconstructing 3D thin structures. Extensive validations on a variety of thin structures show that our method achieves accurate camera pose estimation and faithful reconstruction of 3D thin structures with complex shape and topology at a level that has not been attained by other existing reconstruction methods.Comment: Accepted by SIGGRAPH 202