Extraction of Airways with Probabilistic State-space Models and Bayesian Smoothing

Segmenting tree structures is common in several image processing applications. In medical image analysis, reliable segmentations of airways, vessels, neurons and other tree structures can enable important clinical applications. We present a framework for tracking tree structures comprising of elongated branches using probabilistic state-space models and Bayesian smoothing. Unlike most existing methods that proceed with sequential tracking of branches, we present an exploratory method, that is less sensitive to local anomalies in the data due to acquisition noise and/or interfering structures. The evolution of individual branches is modelled using a process model and the observed data is incorporated into the update step of the Bayesian smoother using a measurement model that is based on a multi-scale blob detector. Bayesian smoothing is performed using the RTS (Rauch-Tung-Striebel) smoother, which provides Gaussian density estimates of branch states at each tracking step. We select likely branch seed points automatically based on the response of the blob detection and track from all such seed points using the RTS smoother. We use covariance of the marginal posterior density estimated for each branch to discriminate false positive and true positive branches. The method is evaluated on 3D chest CT scans to track airways. We show that the presented method results in additional branches compared to a baseline method based on region growing on probability images.Comment: 10 pages. Pre-print of the paper accepted at Workshop on Graphs in Biomedical Image Analysis. MICCAI 2017. Quebec Cit

Towards sketch-based exploration of terrain : a feasibility study

CISRG discussion paper ; 1

Avancée de Diabrotica virgifera virgifera [Coleoptera : Chrysomelidae] dans les champs de maïs au Québec et collecte dans le soja à Ottawa, Ontario

La chrysomèle des racines du maïs de l’Ouest, Diabrotica virgifera virgifera, a été trouvée au Québec en septembre 2000 dans la région de la Montérégie. Ceci constitue une extension vers le nord de son aire de répartition. De plus, à Ottawa, quelques individus se sont développés à partir du soja. Ceci constitue la première mention de développement de cet insecte sur du soja au Canada.The western corn rootworm, Diabrotica virgifera virgifera, was found in the Monteregie region in the province of Quebec in September 2000. This finding constitutes a northern extension of the species distribution. Moreover, at Ottawa, some specimens were found developing from soybean plants. This constitutes the first mention of development of this insect on soybean in Canada

Boundary interactions changing operators and dynamical correlations in quantum impurity problems

Recent developments have made possible the computation of equilibrium dynamical correlators in quantum impurity problems. In many situations however, one is rather interested in correlators subject to a non equilibrium initial preparation; this is the case for instance for the occupation probability $P(t)$ in the double well problem of dissipative quantum mechanics (DQM). We show in this paper how to handle this situation in the framework of integrable quantum field theories by introducing ``boundary interactions changing operators''. We determine the properties of these operators by using an axiomatic approach similar in spirit to what is done for form-factors. This allows us to obtain new exact results for $P(t)$; for instance, we find that that at large times (or small $g$), the leading behaviour for g < 1/2} is $P(t)\propto e^{-\Gamma t}\cos\Omega t$, with the universal ratio. $\Omega/\Gamma = \cot {\pi g}/{2(1-g)}$.Comment: 4 pages, revte

3D Geometric Analysis of Tubular Objects based on Surface Normal Accumulation

This paper proposes a simple and efficient method for the reconstruction and extraction of geometric parameters from 3D tubular objects. Our method constructs an image that accumulates surface normal information, then peaks within this image are located by tracking. Finally, the positions of these are optimized to lie precisely on the tubular shape centerline. This method is very versatile, and is able to process various input data types like full or partial mesh acquired from 3D laser scans, 3D height map or discrete volumetric images. The proposed algorithm is simple to implement, contains few parameters and can be computed in linear time with respect to the number of surface faces. Since the extracted tube centerline is accurate, we are able to decompose the tube into rectilinear parts and torus-like parts. This is done with a new linear time 3D torus detection algorithm, which follows the same principle of a previous work on 2D arc circle recognition. Detailed experiments show the versatility, accuracy and robustness of our new method.Comment: in 18th International Conference on Image Analysis and Processing, Sep 2015, Genova, Italy. 201

Anti-Reflection Coating for Nitrogen-Vacancy Optical Measurements in Diamond

We realize anti-reflection (AR) coatings for optical excitation and fluorescence measurements of nitrogen-vacancy (NV) color centers in bulk diamond by depositing quarter-wavelength thick silica layers on the diamondsurface. These AR coatings improve NV-diamond optical measurements by reducing optical reflection at the diamond-air interface from ≈17% to ≈2%, which allows more effective NV optical excitation and more efficient detection of NV fluorescence. We also show that diamondAR coatings eliminate standing-wave interference patterns of excitation laser intensity within bulk diamond, and thereby greatly reduce spatial variations in NV fluorescence, which can degrade spatially resolved magnetic field sensing using NV centers.Engineering and Applied SciencesPhysic

Colored noise in the fractional Hall effect: duality relations and exact results

We study noise in the problem of tunneling between fractional quantum Hall edge states within a four probe geometry. We explore the implications of the strong-weak coupling duality symmetry existent in this problem for relating the various density-density auto-correlations and cross-correlations between the four terminals. We identify correlations that transform as either ``odd'' or ``anti-symmetric'', or ``even'' or ``symmetric'' quantities under duality. We show that the low frequency noise is colored, and that the deviations from white noise are exactly related to the differential conductance. We show explicitly that the relationship between the slope of the low frequency noise spectrum and the differential conductance follows from an identity that holds to {\it all} orders in perturbation theory, supporting the results implied by the duality symmetry. This generalizes the results of quantum supression of the finite frequency noise spectrum to Luttinger liquids and fractional statistics quasiparticles.Comment: 14 pages, 3 figure

Mapping the use of computational modelling and simulation in clinics: A survey

In silico medicine describes the application of computational modelling and simulation (CM&S) to the study, diagnosis, treatment or prevention of a disease. Tremendous research advances have been achieved to facilitate the use of CM&S in clinical applications. Nevertheless, the uptake of CM&S in clinical practice is not always timely and accurately reflected in the literature. A clear view on the current awareness, actual usage and opinions from the clinicians is needed to identify barriers and opportunities for the future of in silico medicine. The aim of this study was capturing the state of CM&S in clinics by means of a survey toward the clinical community. Responses were collected online using the Virtual Physiological Human institute communication channels, engagement with clinical societies, hospitals and individual contacts, between 2020 and 2021. Statistical analyses were done with R. Participants (n = 163) responded from all over the world. Clinicians were mostly aged between 35 and 64 years-old, with heterogeneous levels of experience and areas of expertise (i.e., 48% cardiology, 13% musculoskeletal, 8% general surgery, 5% paediatrics). The CM&S terms “Personalised medicine” and “Patient-specific modelling” were the most well-known within the respondents. “In silico clinical trials” and “Digital Twin” were the least known. The familiarity with different methods depended on the medical specialty. CM&S was used in clinics mostly to plan interventions. To date, the usage frequency is still scarce. A well-recognized benefit associated to CM&S is the increased trust in planning procedures. Overall, the recorded level of trust for CM&S is high and not proportional to awareness level. The main barriers appear to be access to computing resources, perception that CM&S is slow. Importantly, clinicians see a role for CM&S expertise in their team in the future. This survey offers a snapshot of the current situation of CM&S in clinics. Although the sample size and representativity could be increased, the results provide the community with actionable data to build a responsible strategy for accelerating a positive uptake of in silico medicine. New iterations and follow-up activities will track the evolution of responses over time and contribute to strengthen the engagement with the medical community

MASCARA-2 b: A hot Jupiter transiting the mV=7.6m_V=7.6 A-star HD185603

In this paper we present MASCARA-2 b, a hot Jupiter transiting the $m_V=7.6$ A2 star HD 185603. Since early 2015, MASCARA has taken more than 1.6 million flux measurements of the star, corresponding to a total of almost 3000 hours of observations, revealing a periodic dimming in the flux with a depth of $1.3\%$. Photometric follow-up observations were performed with the NITES and IAC80 telescopes and spectroscopic measurements were obtained with the Hertzsprung SONG telescope. We find MASCARA-2 b orbits HD 185603 with a period of $3.474119^{+0.000005}_{-0.000006}~\rm{days}$ at a distance of $0.057 \pm 0.006~\rm{AU}$, has a radius of $1.83 \pm 0.07~\rm{R}_{\rm{J}}$ and place a $99\%$ upper limit on the mass of $< 17~\rm{M}_{\rm{J}}$. HD 185603 is a rapidly rotating early-type star with an effective temperature of $8980^{+90}_{-130}~\rm{K}$ and a mass and radius of $1.89^{+0.06}_{-0.05}~M_\odot$, $1.60 \pm 0.06~R_\odot$, respectively. Contrary to most other hot Jupiters transiting early-type stars, the projected planet orbital axis and stellar spin axis are found to be aligned with $\lambda=0.6 \pm 4^\circ$. The brightness of the host star and the high equilibrium temperature, $2260 \pm 50~\rm{K}$, of MASCARA-2 b make it a suitable target for atmospheric studies from the ground and space. Of particular interest is the detection of TiO, which has recently been detected in the similarly hot planets WASP-33 b and WASP-19 b.Comment: 8 pages, 4 figures, Accepted for publication in A&