Stochastic rank correlation: a robust merit function for 2D/3D registration of image data obtained at different energies

In this article, the authors evaluate a merit function for 2D/3D registration called stochastic rank correlation (SRC). SRC is characterized by the fact that differences in image intensity do not influence the registration result; it therefore combines the numerical advantages of cross correlation (CC)-type merit functions with the flexibility of mutual-information-type merit functions. The basic idea is that registration is achieved on a random subset of the image, which allows for an efficient computation of Spearman's rank correlation coefficient. This measure is, by nature, invariant to monotonic intensity transforms in the images under comparison, which renders it an ideal solution for intramodal images acquired at different energy levels as encountered in intrafractional kV imaging in image-guided radiotherapy. Initial evaluation was undertaken using a 2D/3D registration reference image dataset of a cadaver spine. Even with no radiometric calibration, SRC shows a significant improvement in robustness and stability compared to CC. Pattern intensity, another merit function that was evaluated for comparison, gave rather poor results due to its limited convergence range. The time required for SRC with 5% image content compares well to the other merit functions; increasing the image content does not significantly influence the algorithm accuracy. The authors conclude that SRC is a promising measure for 2D/3D registration in IGRT and image-guided therapy in general.

Evaluation of Binocular Eye Trackers and Algorithms for 3D Gaze Interaction in Virtual Reality Environments

Tracking user’s visual attention is a fundamental aspect in novel human-computer interaction paradigms found in Virtual Reality. For example, multimodal interfaces or dialogue-based communications with virtual and real agents greatly benefit from the analysis of the user’s visual attention as a vital source for deictic references or turn-taking signals. Current approaches to determine visual attention rely primarily on monocular eye trackers. Hence they are restricted to the interpretation of two-dimensional fixations relative to a defined area of projection. The study presented in this article compares precision, accuracy and application performance of two binocular eye tracking devices. Two algorithms are compared which derive depth information as required for visual attention-based 3D interfaces. This information is further applied to an improved VR selection task in which a binocular eye tracker and an adaptive neural network algorithm is used during the disambiguation of partly occluded objects.

An Empirical Study of Non-Rigid Surface Feature Matching of Human from 3D Video

This paper presents an empirical study of affine invariant feature detectors to perform matching on video sequences of people with non-rigid surface deformation. Recent advances in feature detection and wide baseline matching have focused on static scenes. Video frames of human movement capture highly non-rigid deformation such as loose hair, cloth creases, skin stretching and free flowing clothing. This study evaluates the performance of six widely used feature detectors for sparse temporal correspondence on single view and multiple view video sequences. Quantitative evaluation is performed of both the number of features detected and their temporal matching against and without ground truth correspondence. Recall-accuracy analysis of feature matching is reported for temporal correspondence on single view and multiple view sequences of people with variation in clothing and movement. This analysis identifies that existing feature detection and matching algorithms are unreliable for fast movement with common clothing.

Bayesian Approach to Spectral Function Reconstruction for Euclidean Quantum Field Theories

We present a novel approach to the inference of spectral functions from Euclidean time correlator data that makes close contact with modern Bayesian concepts. Our method differs significantly from the maximum entropy method (MEM). A new set of axioms is postulated for the prior probability, leading to an improved expression, which is devoid of the asymptotically flat directions present in the Shanon-Jaynes entropy. Hyperparameters are integrated out explicitly, liberating us from the Gaussian approximations underlying the evidence approach of the maximum entropy method. We present a realistic test of our method in the context of the nonperturbative extraction of the heavy quark potential. Based on hard-thermal-loop correlator mock data, we establish firm requirements in the number of data points and their accuracy for a successful extraction of the potential from lattice QCD. Finally we reinvestigate quenched lattice QCD correlators from a previous study and provide an improved potential estimation at T2.33TC.

3D volumetric intensity reconsturction from 2D x-ray images using partial least squares regression

Reconstruction of shape and intensity from 2D x-ray images has drawn more and more attentions. Previously introduced work suffers from the long computing time due to its iterative optimization characteristics and the requirement of generating digitally reconstructed radiographs within each iteration. In this paper, we propose a novel method which uses a patient-specific 3D surface model reconstructed from 2D x-ray images as a surrogate to get a patient-specific volumetric intensity reconstruction via partial least squares regression. No DRR generation is needed. The method was validated on 20 cadaveric proximal femurs by performing a leave-one-out study. Qualitative and quantitative results demonstrated the efficacy of the present method. Compared to the existing work, the present method has the advantage of much shorter computing time and can be applied to both DXA images as well as conventional x-ray images, which may hold the potentials to be applied to clinical routine task such as total hip arthroplasty (THA).

Laparoscopic computer-navigated ablation of liver metastases

Objective In order to benefit from the obvious advantages of minimally invasive liver surgery there is a need to develop high precision tools for intraoperative anatomical orientation, navigation and safety control. In a pilot study we adapted a newly developed system for computer-assisted liver surgery (CALS) in terms of accuracy and technical feasibility to the specific requirements of laparoscopy. Here, we present practical aspects related to laparoscopic computer assisted liver surgery (LCALS). Methods Our video relates to a patient presenting with 3 colorectal liver metastases in Seg. II, III and IVa who was selected in an appropriate oncological setting for LCALS using the CAScination system combined with 3D MEVIS reconstruction. After minimal laparoscopic mobilization of the liver, a 4- landmark registration method was applied to enable navigation. Placement of microwave needles was performed using the targeting module of the navigation system and correct needle positioning was confirmed by intraoperative sonography. Ablation of each lesion was carried out by application of microwave energy at 100 Watts for 1 minute. Results To acquire an accurate (less 0.5 cm) registration, 4 registration cycles were necessary. In total, seven minutes were required to accomplish precise registration. Successful ablation with complete response in all treated areas was assessed by intraoperative sonography and confirmed by postoperative CT scan. Conclusions This teaching video demonstrates the theoretical and practical key points of LCALS with a special emphasis on preoperative planning, intraoperative registration and accuracy testing by laparoscopic methodology. In contrast to mere ultrasound-guided ablation of liver lesions, LCALS offers a more dimensional targeting and higher safety control. This is currently also in routine use to treat vanishing lesions and other difficult to target focal lesions within the liver.

EVALUATION OF THE QUANTITATIVE ACCURACY OF A COMMERCIALLY-AVAILABLE POSITRON EMISSION MAMMOGRAPHY SCANNER

Objective: The PEM Flex Solo II (Naviscan, Inc., San Diego, CA) is currently the only commercially-available positron emission mammography (PEM) scanner. This scanner does not apply corrections for count rate effects, attenuation or scatter during image reconstruction, potentially affecting the quantitative accuracy of images. This work measures the overall quantitative accuracy of the PEM Flex system, and determines the contributions of error due to count rate effects, attenuation and scatter. Materials and Methods: Gelatin phantoms were designed to simulate breasts of different sizes (4 – 12 cm thick) with varying uniform background activity concentration (0.007 – 0.5 μCi/cc), cysts and lesions (2:1, 5:1, 10:1 lesion-to-background ratios). The overall error was calculated from ROI measurements in the phantoms with a clinically relevant background activity concentration (0.065 μCi/cc). The error due to count rate effects was determined by comparing the overall error at multiple background activity concentrations to the error at 0.007 μCi/cc. A point source and cold gelatin phantoms were used to assess the errors due to attenuation and scatter. The maximum pixel values in gelatin and in air were compared to determine the effect of attenuation. Scatter was evaluated by comparing the sum of all pixel values in gelatin and in air. Results: The overall error in the background was found to be negative in phantoms of all thicknesses, with the exception of the 4-cm thick phantoms (0%±7%), and it increased with thickness (-34%±6% for the 12-cm phantoms). All lesions exhibited large negative error (-22% for the 2:1 lesions in the 4-cm phantom) which increased with thickness and with lesion-to-background ratio (-85% for the 10:1 lesions in the 12-cm phantoms). The error due to count rate in phantoms with 0.065 μCi/cc background was negative (-23%±6% for 4-cm thickness) and decreased with thickness (-7%±7% for 12 cm). Attenuation was a substantial source of negative error and increased with thickness (-51%±10% to -77% ±4% in 4 to 12 cm phantoms, respectively). Scatter contributed a relatively constant amount of positive error (+23%±11%) for all thicknesses. Conclusion: Applying corrections for count rate, attenuation and scatter will be essential for the PEM Flex Solo II to be able to produce quantitatively accurate images.

3D MPRAGE improves classification of cortical lesions in multiple sclerosis.

BACKGROUND: Gray matter lesions are known to be common in multiple sclerosis (MS) and are suspected to play an important role in disease progression and clinical disability. A combination of magnetic resonance imaging (MRI) techniques, double-inversion recovery (DIR), and phase-sensitive inversion recovery (PSIR), has been used for detection and classification of cortical lesions. This study shows that high-resolution three-dimensional (3D) magnetization-prepared rapid acquisition with gradient echo (MPRAGE) improves the classification of cortical lesions by allowing more accurate anatomic localization of lesion morphology. METHODS: 11 patients with MS with previously identified cortical lesions were scanned using DIR, PSIR, and 3D MPRAGE. Lesions were identified on DIR and PSIR and classified as purely intracortical or mixed. MPRAGE images were then examined, and lesions were re-classified based on the new information. RESULTS: The high signal-to-noise ratio, fine anatomic detail, and clear gray-white matter tissue contrast seen in the MPRAGE images provided superior delineation of lesion borders and surrounding gray-white matter junction, improving classification accuracy. 119 lesions were identified as either intracortical or mixed on DIR/PSIR. In 89 cases, MPRAGE confirmed the classification by DIR/PSIR. In 30 cases, MPRAGE overturned the original classification. CONCLUSION: Improved classification of cortical lesions was realized by inclusion of high-spatial resolution 3D MPRAGE. This sequence provides unique detail on lesion morphology that is necessary for accurate classification.

Quantitative 3D strain analysis in analogue experiments: Integration of X-ray computed tomography and digital volume correlation techniques

The combination of scaled analogue experiments, material mechanics, X-ray computed tomography (XRCT) and Digital Volume Correlation techniques (DVC) is a powerful new tool not only to examine the 3 dimensional structure and kinematic evolution of complex deformation structures in scaled analogue experiments, but also to fully quantify their spatial strain distribution and complete strain history. Digital image correlation (DIC) is an important advance in quantitative physical modelling and helps to understand non-linear deformation processes. Optical non-intrusive (DIC) techniques enable the quantification of localised and distributed deformation in analogue experiments based either on images taken through transparent sidewalls (2D DIC) or on surface views (3D DIC). X-ray computed tomography (XRCT) analysis permits the non-destructive visualisation of the internal structure and kinematic evolution of scaled analogue experiments simulating tectonic evolution of complex geological structures. The combination of XRCT sectional image data of analogue experiments with 2D DIC only allows quantification of 2D displacement and strain components in section direction. This completely omits the potential of CT experiments for full 3D strain analysis of complex, non-cylindrical deformation structures. In this study, we apply digital volume correlation (DVC) techniques on XRCT scan data of “solid” analogue experiments to fully quantify the internal displacement and strain in 3 dimensions over time. Our first results indicate that the application of DVC techniques on XRCT volume data can successfully be used to quantify the 3D spatial and temporal strain patterns inside analogue experiments. We demonstrate the potential of combining DVC techniques and XRCT volume imaging for 3D strain analysis of a contractional experiment simulating the development of a non-cylindrical pop-up structure. Furthermore, we discuss various options for optimisation of granular materials, pattern generation, and data acquisition for increased resolution and accuracy of the strain results. Three-dimensional strain analysis of analogue models is of particular interest for geological and seismic interpretations of complex, non-cylindrical geological structures. The volume strain data enable the analysis of the large-scale and small-scale strain history of geological structures.

Evaluating the Quality and Accuracy of TanDEM-X Digital Elevation Models at Archaeological Sites in the Cilician Plain, Turkey

Satellite remote sensing provides a powerful instrument for mapping and monitoring traces of historical settlements and infrastructure, not only in distant areas and crisis regions. It helps archaeologists to embed their findings from field surveys into the broader context of the landscape. With the start of the TanDEM-X mission, spatially explicit 3D-information is available to researchers at an unprecedented resolution worldwide. We examined different experimental TanDEM-X digital elevation models (DEM) that were processed from two different imaging modes (Stripmap/High Resolution Spotlight) using the operational alternating bistatic acquisition mode. The quality and accuracy of the experimental DEM products was compared to other available DEM products and a high precision archaeological field survey. The results indicate the potential of TanDEM-X Stripmap (SM) data for mapping surface elements at regional scale. For the alluvial plain of Cilicia, a suspected palaeochannel could be reconstructed. At the local scale, DEM products from TanDEM-X High Resolution Spotlight (HS) mode were processed at 2 m spatial resolution using a merge of two monostatic/bistatic interferograms. The absolute and relative vertical accuracy of the outcome meet the specification of high resolution elevation data (HRE) standards from the National System for Geospatial Intelligence (NSG) at the HRE20 level.

Detergent-induced stabilization and improved 3D map of the human heteromeric amino acid transporter 4F2hc-LAT2.

Human heteromeric amino acid transporters (HATs) are membrane protein complexes that facilitate the transport of specific amino acids across cell membranes. Loss of function or overexpression of these transporters is implicated in several human diseases such as renal aminoacidurias and cancer. HATs are composed of two subunits, a heavy and a light subunit, that are covalently connected by a disulphide bridge. Light subunits catalyse amino acid transport and consist of twelve transmembrane α-helix domains. Heavy subunits are type II membrane N-glycoproteins with a large extracellular domain and are involved in the trafficking of the complex to the plasma membrane. Structural information on HATs is scarce because of the difficulty in heterologous overexpression. Recently, we had a major breakthrough with the overexpression of a recombinant HAT, 4F2hc-LAT2, in the methylotrophic yeast Pichia pastoris. Microgram amounts of purified protein made possible the reconstruction of the first 3D map of a human HAT by negative-stain transmission electron microscopy. Here we report the important stabilization of purified human 4F2hc-LAT2 using a combination of two detergents, i.e., n-dodecyl-β-D-maltopyranoside and lauryl maltose neopentyl glycol, and cholesteryl hemisuccinate. The superior quality and stability of purified 4F2hc-LAT2 allowed the measurement of substrate binding by scintillation proximity assay. In addition, an improved 3D map of this HAT could be obtained. The detergent-induced stabilization of the purified human 4F2hc-LAT2 complex presented here paves the way towards its crystallization and structure determination at high-resolution, and thus the elucidation of the working mechanism of this important protein complex at the molecular level.

MR Angiography at 3 Tesla to Assess Proximal Internal Carotid Artery Stenoses: Contrast-Enhanced or 3D Time-of-Flight MR Angiography?

PURPOSE The aim of this study was to compare the diagnostic accuracy of 3D time-of-flight (TOF-MRA) and contrast-enhanced (CE-MRA) magnetic resonance angiography at 3 T for detection and quantification of proximal high-grade stenosis using multidetector computed tomography angiography (MDCTA) as reference standard. METHODS The institutional ethics committee approved this prospective study. A total of 41 patients suspected of having internal carotid artery (ICA) stenosis underwent both MDCTA and MRA. CE-MRA and TOF-MRA were performed using a 3.0-T imager with a dedicated eight-element cervical coil. ICA stenoses were measured according to the North American Symptomatic Carotid Endarterectomy Trial criteria and categorized as 0-25 % (minimal), 25-50 % (mild), 50-69 % (moderate), 70-99 % (high grade), and 100 % (occlusion). Sensitivity and specificity for the detection of high-grade ICA stenoses (70-99 %) and ICA occlusions were determined. In addition, intermodality agreement was assessed with κ-statistics for detection of high-grade ICA stenoses (70-99 %) and ICA occlusions. RESULTS A total of 80 carotid arteries of 41 patients were reviewed. Two previously stented ICAs were excluded from analysis. On MDCTA, 7 ICAs were occluded, 12 ICAs presented with and 63 without a high-grade ICA stenosis (70-99 %). For detecting 70-99 % stenosis, both 3D TOF-MRA and CE-MRA were 91.7 % sensitive and 98.5 % specific, respectively. Both MRA techniques were highly sensitive (100 %), and specific (CE-MRA, 100 %; TOF-MRA, 98.7 %) for the detection of ICA occlusion. However, TOF-MRA misclassified one high-grade stenosis as occlusion. Intermodality agreement for detection of 70-99 % ICA stenoses was excellent between TOF-MRA and CE-MRA [κ = 0.902, 95 % confidence interval (CI) = 0.769-1.000], TOF-MRA and MDCTA (κ = 0.902, 95 % CI = 0.769-1.000), and CE-MRA and MDCTA (κ = 0.902, 95 % CI = 0.769-1.000). CONCLUSION Both 3D TOF-MRA and CE-MRA at 3 T are reliable tools for detecting high-grade proximal ICA stenoses (70-99 %). 3D TOF-MRA might misclassify pseudo-occlusions as complete occlusions. If there are no contraindications for CE-MRA, CE-MRA is recommended as primary MR imaging modality.

Automated 3D Lumbar Intervertebral Disc Segmentation from MRI Data Sets

This paper proposed an automated 3D lumbar intervertebral disc (IVD) segmentation strategy from MRI data. Starting from two user supplied landmarks, the geometrical parameters of all lumbar vertebral bodies and intervertebral discs are automatically extracted from a mid-sagittal slice using a graphical model based approach. After that, a three-dimensional (3D) variable-radius soft tube model of the lumbar spine column is built to guide the 3D disc segmentation. The disc segmentation is achieved as a multi-kernel diffeomorphic registration between a 3D template of the disc and the observed MRI data. Experiments on 15 patient data sets showed the robustness and the accuracy of the proposed algorithm.

Electron reconstruction and identification efficiency measurements with the ATLAS detector using the 2011 LHC proton-proton collision data

Many of the interesting physics processes to be measured at the LHC have a signature involving one or more isolated electrons. The electron reconstruction and identification efficiencies of the ATLAS detector at the LHC have been evaluated using proton–proton collision data collected in 2011 at √s = 7 TeV and corresponding to an integrated luminosity of 4.7 fb−1. Tag-and-probe methods using events with leptonic decays of W and Z bosons and J/ψ mesons are employed to benchmark these performance parameters. The combination of all measurements results in identification efficiencies determined with an accuracy at the few per mil level for electron transverse energy greater than 30 GeV.

A chrysophyte-based quantitative reconstruction of winter severity from varved lake sediments in NE Poland during the past millennium and its relationship to natural climate variability

Chrysophyte cysts are recognized as powerful proxies of cold-season temperatures. In this paper we use the relationship between chrysophyte assemblages and the number of days below 4 °C (DB4 °C) in the epilimnion of a lake in northern Poland to develop a transfer function and to reconstruct winter severity in Poland for the last millennium. DB4 °C is a climate variable related to the length of the winter. Multivariate ordination techniques were used to study the distribution of chrysophytes from sediment traps of 37 low-land lakes distributed along a variety of environmental and climatic gradients in northern Poland. Of all the environmental variables measured, stepwise variable selection and individual Redundancy analyses (RDA) identified DB4 °C as the most important variable for chrysophytes, explaining a portion of variance independent of variables related to water chemistry (conductivity, chlorides, K, sulfates), which were also important. A quantitative transfer function was created to estimate DB4 °C from sedimentary assemblages using partial least square regression (PLS). The two-component model (PLS-2) had a coefficient of determination of View the MathML sourceRcross2 = 0.58, with root mean squared error of prediction (RMSEP, based on leave-one-out) of 3.41 days. The resulting transfer function was applied to an annually-varved sediment core from Lake Żabińskie, providing a new sub-decadal quantitative reconstruction of DB4 °C with high chronological accuracy for the period AD 1000–2010. During Medieval Times (AD 1180–1440) winters were generally shorter (warmer) except for a decade with very long and severe winters around AD 1260–1270 (following the AD 1258 volcanic eruption). The 16th and 17th centuries and the beginning of the 19th century experienced very long severe winters. Comparison with other European cold-season reconstructions and atmospheric indices for this region indicates that large parts of the winter variability (reconstructed DB4 °C) is due to the interplay between the oscillations of the zonal flow controlled by the North Atlantic Oscillation (NAO) and the influence of continental anticyclonic systems (Siberian High, East Atlantic/Western Russia pattern). Differences with other European records are attributed to geographic climatological differences between Poland and Western Europe (Low Countries, Alps). Striking correspondence between the combined volcanic and solar forcing and the DB4 °C reconstruction prior to the 20th century suggests that winter climate in Poland responds mostly to natural forced variability (volcanic and solar) and the influence of unforced variability is low.