Accurate geometry reconstruction of vascular structures using implicit splines

3-D visualization of blood vessel from standard medical datasets (e.g. CT or MRI) play an important role in many clinical situations, including the diagnosis of vessel stenosis, virtual angioscopy, vascular surgery planning and computer aided vascular surgery. However, unlike other human organs, the vasculature system is a very complex network of vessel, which makes it a very challenging task to perform its 3-D visualization. Conventional techniques of medical volume data visualization are in general not well-suited for the above-mentioned tasks. This problem can be solved by reconstructing vascular geometry. Although various methods have been proposed for reconstructing vascular structures, most of these approaches are model-based, and are usually too ideal to correctly represent the actual variation presented by the cross-sections of a vascular structure. In addition, the underlying shape is usually expressed as polygonal meshes or in parametric forms, which is very inconvenient for implementing ramification of branching. As a result, the reconstructed geometries are not suitable for computer aided diagnosis and computer guided minimally invasive vascular surgery. In this research, we develop a set of techniques associated with the geometry reconstruction of vasculatures, including segmentation, modelling, reconstruction, exploration and rendering of vascular structures. The reconstructed geometry can not only help to greatly enhance the visual quality of 3-D vascular structures, but also provide an actual geometric representation of vasculatures, which can provide various benefits. The key findings of this research are as follows: 1. A localized hybrid level-set method of segmentation has been developed to extract the vascular structures from 3-D medical datasets. 2. A skeleton-based implicit modelling technique has been proposed and applied to the reconstruction of vasculatures, which can achieve an accurate geometric reconstruction of the vascular structures as implicit surfaces in an analytical form. 3. An accelerating technique using modern GPU (Graphics Processing Unit) is devised and applied to rendering the implicitly represented vasculatures. 4. The implicitly modelled vasculature is investigated for the application of virtual angioscopy

Semiautomatic Detection of Scoliotic Rib Borders From Posteroanterior Chest Radiographs

3-D assessment of scoliotic deformities relies on an accurate 3-D reconstruction of bone structures from biplanar X-rays, which requires a precise detection and matching of anatomical structures in both views. In this paper, we propose a novel semiautomated technique for detecting complete scoliotic rib borders from PA-0° and PA-20° chest radiographs, by using an edge-following approach with multiple-path branching and oriented filtering. Edge-following processes are initiated from user starting points along upper and lower rib edges and the final rib border is obtained by finding the most parallel pair among detected edges. The method is based on a perceptual analysis leading to the assumption that no matter how bent a scoliotic rib is, it will always present relatively parallel upper and lower edges. The proposed method was tested on 44 chest radiographs of scoliotic patients and was validated by comparing pixels from all detected rib borders against their reference locations taken from the associated manually delineated rib borders. The overall 2-D detection accuracy was 2.64 ± 1.21 pixels. Comparing this accuracy level to reported results in the literature shows that the proposed method is very well suited for precisely detecting borders of scoliotic ribs from PA-0° and PA-20° chest radiographs.CIHR / IRS

Single-picture reconstruction and rendering of trees for plausible vegetation synthesis

State-of-the-art approaches for tree reconstruction either put limiting constraints on the input side (requiring multiple photographs, a scanned point cloud or intensive user input) or provide a representation only suitable for front views of the tree. In this paper we present a complete pipeline for synthesizing and rendering detailed trees from a single photograph with minimal user effort. Since the overall shape and appearance of each tree is recovered from a single photograph of the tree crown, artists can benefit from georeferenced images to populate landscapes with native tree species. A key element of our approach is a compact representation of dense tree crowns through a radial distance map. Our first contribution is an automatic algorithm for generating such representations from a single exemplar image of a tree. We create a rough estimate of the crown shape by solving a thin-plate energy minimization problem, and then add detail through a simplified shape-from-shading approach. The use of seamless texture synthesis results in an image-based representation that can be rendered from arbitrary view directions at different levels of detail. Distant trees benefit from an output-sensitive algorithm inspired on relief mapping. For close-up trees we use a billboard cloud where leaflets are distributed inside the crown shape through a space colonization algorithm. In both cases our representation ensures efficient preservation of the crown shape. Major benefits of our approach include: it recovers the overall shape from a single tree image, involves no tree modeling knowledge and minimal authoring effort, and the associated image-based representation is easy to compress and thus suitable for network streaming.Peer ReviewedPostprint (author's final draft

Accurate Prediction of Core Properties for Chiral Molecules using Pseudo Potentials

Pseudo potentials (PPs) constitute perhaps the most common way to treat relativity, often in a formally non-relativistic framework, and reduce the electronic structure to the chemically relevant part. The drawback is that orbitals obtained in this picture (called pseudo orbitals (POs)) show a reduced nodal structure and altered amplitude in the vicinity of the nucleus, when compared to the corresponding molecular orbitals (MOs). Thus expectation values of operators localized in the spatial core region that are calculated with POs, deviate significantly from the same expectation values calculated with all-electron (AE) MOs. This study describes the reconstruction of AE MOs from POs, with a focus on POs generated by energy consistent pseudo Hamiltonians. The method reintroduces the nodal structure into the POs, thus providing an inexpensive and easily implementable method that allows to use nonrelativistic, efficiently calculated POs for good estimates of expectation values of core-like properties. The discussion of the method proceeds in two parts: Firstly, the reconstruction scheme is developed for atomic cases. Secondly, the scheme is discussed in the context of MO reconstruction and successfully applied to numerous numerical examples. Starting from the equations of the state-averaged multi-configuration self- consistent field method, used for the generation of energy consistent pseudo potentials, the electronic spectrum of the many-electron Hamiltonian is linked to the spectrum of the effective one-electron Fock operator by means of various models systems. This relation and the Topp–Hopfield–Kramers theorem, are used to show the shape-consistency of energy-consistent POs for atomic systems. Shape-consistency describes POs that follow distinct AOs exactly outside a core-radius r_core . In the cases presented here, shape-consistency holds to a high degree and it follows that in atomic systems every PO has one distinct partner in the set of AOs. The overlap integral between these two orbitals is close to one, as it is determined mainly by the spatial orbital parts outside r_core . Expanding, e.g., a 5s PO in occupied AOs, the 5s AOs will have the highest contribution. The POs itself contains contributions from high-energy unoccupied AOs as well (e.g. 15s), which damp the nodal structure of the POs near the nucleus. Consequently, neglecting contributions from unoccupied orbitals in a projection of the POs reintroduces the nodal structure. This approach is not directly suitable for the reconstruction of MOs, as they often need to be expanded in a full set of AOs at each atomic center, including all unoccupied orbitals, to properly account for the electron density distribution in the molecule. However, it is shown that the occupied MOs are well described by occupied and low-energy unoccupied AOs only and a mapping of the POs onto a basis containing only these orbitals reconstructs the nodal structure of the MO. The approach uses only standard integrals available in most quantum chemistry programs. The computational cost of these integrals scales with N^2 , where N is the number of basis functions. The most time consuming step is a Gram-Schmidt orthogonalization, which scales in this implementation with MN^2 , M being the number of reconstructed orbitals. The reconstruction method is subsequently tested: Valence orbitals of atomic, closed-shell systems were reconstructed numerically exactly. The influence of numerical parameters is investigated using the molecule BaF . It is shown that the method is basis set dependent: One has to ensure that the PO basis can be expanded exactly in the basis of AOs. Violating this rule of thumb may degrade the quality of reconstructed orbitals. Additionally, the representation of MOs by a linear combination of occupied and unoccupied AOs is investigated. For the exemplary systems, the shells included in the fitting procedure of the PP were sufficient. Reconstruction of the alkaline earth monofluorides showed that periodic trends can be reconstructed as well. Scaling of hyperfine structure parameters with increasing atomic number is discussed. For hydrogenic atoms, the scaling should be linear, whereas small deviations from the linear behavior were observed for molecules. The scaling laws computed from reconstructed and reference orbitals were almost identical. In this context, the failure of commonly used relativistic enhancement factors beyond atomic number 100 is discussed. Applicability of the method is also tested on parity violating properties for which the main contribution is generated by the valence orbitals near the nucleus. Symmetry-independence of the method is shown by successful reconstruction of orbitals of the tetrahedral PbCl_4 and chiral NWHClF. The reliable reconstruction of chemical trends is shown with the help of the NWHClF derivatives NWHBrF and NWHFI. The study of chiral compounds as, e.g., NWHClF and its group 17 derivatives, which have been proposed as paradigm for the detection of parity-violation in chiral molecules, remains of great importance. Especially the direct determination of absolute configuration of chiral centers is still non-trivial. The author contributed to this field with a self-written molecular dynamics (MD) program to simulate Coulomb explosions and thus to provide an insight especially into the early explosion stages directly after an instantaneous multi-ionization of the molecule CHBrClF, comparable to experiments using the Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS) technique. An algorithm for the determination of the investigated molecule’s absolute configuration from time-of-flight data and detection locations of molecular fragments is included in the program. The program was used to generate experiment-equivalent data which allowed for the first time the investigation of non-racemic mixtures by the analysis routines of the experiment. The MD program includes harmonic and anharmonic bond potentials. A charge-exchange model can model partial charges in early phases of the Coulomb explosion. Furthermore, Born–Oppenheimer MD simulations and statistical models are used to explain the relative abundance of products belonging to competing reaction channels, as obtained by photoion coincidence measurements. Additionally, qualitative statements about reaction branching ratios are made by comparing the partition functions of involved degrees of freedom. Analytic equations for partition functions of simple models are used to provide a simple formula allowing fast estimates of reaction branching ratios

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

BackgroundSingle-cell transcriptomics allows researchers to investigate complex communities of heterogeneous cells. It can be applied to stem cells and their descendants in order to chart the progression from multipotent progenitors to fully differentiated cells. While a variety of statistical and computational methods have been proposed for inferring cell lineages, the problem of accurately characterizing multiple branching lineages remains difficult to solve.ResultsWe introduce Slingshot, a novel method for inferring cell lineages and pseudotimes from single-cell gene expression data. In previously published datasets, Slingshot correctly identifies the biological signal for one to three branching trajectories. Additionally, our simulation study shows that Slingshot infers more accurate pseudotimes than other leading methods.ConclusionsSlingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the identification of dynamic temporal gene expression

Higgs Physics at future Linear Colliders - A Case for precise Vertexing

The discovery of a Higgs boson by the experiments at the LHC marks a major breakthrough in particle physics, with far-reaching consequences for our understanding of the fundamental principles of our Universe. To fully explore this unique particle, experiments at high-energy electron-positron colliders are being planned, providing substantial added benefit over the capabilities of the LHC alone, such as model-independent measurements of couplings, constraints on invisible decays and precise measurements of the self-coupling. This contribution summarizes the Higgs physics program at such future facilities, highlighting in particular also the role of precise vertexing in achieving the ambitious goals of these experiments.Comment: 9 pages, 4 figures, to be published in the proceedings of the 22nd International Workshop on Vertex Detectors VERTEX 2013, Lake Starnberg, Germany, September 2013, v2 updated references. arXiv admin note: substantial text overlap with arXiv:1211.724