GIFT-Grab: Real-time C++ and Python multi-channel video capture, processing and encoding API

GIFT-Grab is an open-source API for acquiring, processing and encoding video streams in real time. GIFT-Grab supports video acquisition using various frame-grabber hardware as well as from standard-compliant network streams and video files. The current GIFT-Grab release allows for multi-channel video acquisition and encoding at the maximum frame rate of supported hardware – 60 frames per second (fps). GIFT-Grab builds on well-established highly configurable multimedia libraries including FFmpeg and OpenCV. GIFT-Grab exposes a simplified high-level API, aimed at facilitating integration into client applications with minimal coding effort. The core implementation of GIFT-Grab is in C++11. GIFT-Grab also features a Python API compatible with the widely used scientific computing packages NumPy and SciPy. GIFT-Grab was developed for capturing multiple simultaneous intra-operative video streams from medical imaging devices. Yet due to the ubiquity of video processing in research, GIFT-Grab can be used in many other areas. GIFT-Grab is hosted and managed on the software repository of the Centre for Medical Image Computing (CMIC) at University College London, and is also mirrored on GitHub. In addition it is available for installation from the Python Package Index (PyPI) via the pip installation tool

Dynamically balanced online random forests for interactive scribble-based segmentation

Interactive scribble-and-learning-based segmentation is attractive for its good performance and reduced number of user interaction. Scribbles for foreground and background are often imbalanced. With the arrival of new scribbles,the imbalance ratio may change largely. Failing to deal with imbalanced training data and a changing imbalance ratio may lead to a decreased sensitivity and accuracy for segmentation. We propose a generic Dynamically Balanced Online Random Forest (DyBa ORF) to deal with these problems,with a combination of a dynamically balanced online Bagging method and a tree growing and shrinking strategy to update the random forests. We validated DyBa ORF on UCI machine learning data sets and applied it to two different clinical applications: 2D segmentation of the placenta from fetal MRI and adult lungs from radiographic images. Experiments show it outperforms traditional ORF in dealing with imbalanced data with a changing imbalance ratio,while maintaining a comparable accuracy and a higher efficiency compared with its offline counterpart. Our results demonstrate that DyBa ORF is more suitable than existing ORF for learning-based interactive image segmentation

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

Level Crossing for Hot Sphalerons

We study the spectrum of the Dirac Hamiltonian in the presence of high temperature sphaleron-like fluctuations of the electroweak gauge and Higgs fields, relevant for the conditions prevailing in the early universe. The fluctuations are created by numerical lattice simulations. It is shown that a change in Chern-Simons number by one unit is accompanied by eigenvalues crossing zero and a change of sign of the generalized chirality \tGf= (-1)^{2T+1} \gf which labels these modes. This provides further evidence that the sphaleron-like configurations observed in lattice simulations may be viewed as representing continuum configurations.Comment: Latex file, 29 pages + 13 figure

Perturbative Corrections for Staggered Fermion Bilinears

We calculate the perturbative corrections to fermion bilinears that are used in numerical simulations when extracting weak matrix elements using staggered fermions. This extends previous calculations of Golterman and Smit, and Daniel and Sheard. In particular, we calculate the corrections for non-local bilinears defined in Landau gauge with gauge links excluded. We do this for the simplest operators, i.e. those defined on a $2^4$ hypercube, and for tree level improved operators which live on $4^4$ hypercubes. We also consider gauge invariant operators in which the ``tadpole'' contributions are suppressed by projecting the sums of products of gauge links back in to the gauge group. In all cases, we find that the variation in the size of the perturbative corrections is smaller than those with the gauge invariant unimproved operators. This is most strikingly true for the smeared operators. We investigate the efficacy of the mean-field method of Lepage and Mackenzie at summing up tadpole contributions. In a companion paper we apply these results to four-fermion operators.Comment: 29 pages latex, 4 postscript figures included, UW/PT-92-13 and CEBAF-TH-92-2

Chronic Obstructive Pulmonary Disease: Lobar Analysis with Hyperpolarized 129Xe MR Imaging.

Purpose To compare lobar ventilation and apparent diffusion coefficient (ADC) values obtained with hyperpolarized xenon 129 ((129)Xe) magnetic resonance (MR) imaging to quantitative computed tomography (CT) metrics on a lobar basis and pulmonary function test (PFT) results on a whole-lung basis in patients with chronic obstructive pulmonary disease (COPD). Materials and Methods The study was approved by the National Research Ethics Service Committee; written informed consent was obtained from all patients. Twenty-two patients with COPD (Global Initiative for Chronic Obstructive Lung Disease stage II-IV) underwent hyperpolarized (129)Xe MR imaging at 1.5 T, quantitative CT, and PFTs. Whole-lung and lobar (129)Xe MR imaging parameters were obtained by using automated segmentation of multisection hyperpolarized (129)Xe MR ventilation images and hyperpolarized (129)Xe MR diffusion-weighted images after coregistration to CT scans. Whole-lung and lobar quantitative CT-derived metrics for emphysema and bronchial wall thickness were calculated. Pearson correlation coefficients were used to evaluate the relationship between imaging measures and PFT results. Results Percentage ventilated volume and average ADC at lobar (129)Xe MR imaging showed correlation with percentage emphysema at lobar quantitative CT (r = -0.32, P < .001 and r = 0.75, P < .0001, respectively). The average ADC at whole-lung (129)Xe MR imaging showed moderate correlation with PFT results (percentage predicted transfer factor of the lung for carbon monoxide [Tlco]: r = -0.61, P < .005) and percentage predicted functional residual capacity (r = 0.47, P < .05). Whole-lung quantitative CT percentage emphysema also showed statistically significant correlation with percentage predicted Tlco (r = -0.65, P < .005). Conclusion Lobar ventilation and ADC values obtained from hyperpolarized (129)Xe MR imaging demonstrated correlation with quantitative CT percentage emphysema on a lobar basis and with PFT results on a whole-lung basis. (©) RSNA, 2016

The staggered domain wall fermion method

A different lattice fermion method is introduced. Staggered domain wall fermions are defined in 2n+1 dimensions and describe 2^n flavors of light lattice fermions with exact U(1) x U(1) chiral symmetry in 2n dimensions. As the size of the extra dimension becomes large, 2^n chiral flavors with the same chiral charge are expected to be localized on each boundary and the full SU(2^n) x SU(2^n) flavor chiral symmetry is expected to be recovered. SDWF give a different perspective into the inherent flavor mixing of lattice fermions and by design present an advantage for numerical simulations of lattice QCD thermodynamics. The chiral and topological index properties of the SDWF Dirac operator are investigated. And, there is a surprise ending...Comment: revtex4, 7 figures, minor revisions, 2 references adde