xRing—An R package to identify and measure tree-ring features using X-ray microdensity profiles

Climate influences tree-ring density and ring-density variables extracted from X-ray images have been widely used for climate reconstructions. The R package xRing was developed to identify and measure tree rings on X-ray microdensity profiles automatically. This package is available for free and it offers functions to visualize and calibrate X-ray images, to detect tree-ring borders and to identify earlywood-latewood transition using wood density variations at the inter- and the intra-ring scale. The most important functions are calibrateFilm, detectRings, correctRings, detectEwLw, and getDensity. Outputs of these functions are S3 objects, for which specific methods are provided, including plot and print. The non-linear relationship between optical density of the film and wood density is defined by the function calibrateFilm. The function detectRings detects tree rings using wood density profiles as input. This function uses the difference between local maximum and minimum values to identify tree-ring borders automatically. The correctRings function is used to call a Graphical User Interface (GUI) to visualize and to correct tree-ring borders manually. After correcting tree-ring borders, the detectEwLw function is used to compute earlywood and latewood widths by dividing rings according to relative intra-ring density changes. The getDensity function computes for each tree ring the minimum (maximum) density and the mean earlywood, latewood and whole-ring density. Finally, a list with dataframes with tree-ring width and density variables can be obtained using the function getRwls. One of the major advantages of xRing package is that requires little knowledge of R language, but at the same time it can be easily changed or adapted by experienced users.     

FLIM on a wide field fluorescence microscope

Summary FLIM (Fluorescence Lifetime Imaging Microscopy) is a new tool to detect interaction between proteins. The proteins under investigation are fused with fluorescent donor and acceptor molecules. Interaction between the two proteins is accompanied by direct energy transfer from donor to acceptor (FRET), resulting in a shorter lifetime of the fluorescence emitted by the donor molecule. This change in lifetime is detected by FLIM. Fluorescence lifetime imaging can now be done on a widefield fluorescence microscope by using an attachment that is easy to install and simple to operate. The new LIFA attachment is equipped to use different excitation sources. High brightness modulated LEDs as well as lasers modulated by an Accousto Optical Modulator can be used as excitation light source. A modulated image intensifier with digital camera is used as a detector. Power supplies and signal generator are integrated in one control unit that is connected to the light source, detector and computer. All parameters for image acquisition, processing and viewing are easy accessible in the user interface of the software package that uses a modular structure. Lifetime images showing FRET in MCF7 cells with ErbB1-GFP as donor and Py72/Cy3 as acceptor that were taken at EMBL, Heidelberg are shown.     

EGS_cbct: Simulation of a fan beam CT and RMI phantom for measured HU verification

IntroductionA mathematical 3D model of an existing computed tomography (CT) scanner was created and used in the EGSnrc-based BEAMnrc and egs_cbct Monte Carlo codes. Simulated transmission dose profiles of a RMI-465 phantom were analysed to verify Hounsfield numbers against measured data obtained from the CT scanner.Methods and materialsThe modelled CT unit is based on the design of a Toshiba Aquilion 16 LB CT scanner. As a first step, BEAMnrc simulated the X-ray tube, filters, and secondary collimation to obtain phase space data of the X-ray beam. A bowtie filter was included to create a more uniform beam intensity and to remove the beam hardening effects. In a second step the Interactive Data Language (IDL) code was used to build an EGSPHANT file that contained the RMI phantom which was used in egs_cbct simulations. After simulation a series of profiles were sampled from the detector model and the Feldkamp-Davis-Kress (FDK) algorithm was used to reconstruct transversal images. The results were tested against measured data obtained from CT scans.ResultsThe egs_cbct code can be used for the simulation of a fan beam CT unit. The calculated bowtie filter ensured a uniform flux on the detectors. Good correlation between measured and simulated CT numbers was obtained.ConclusionsIn principle, Monte Carlo codes such as egs_cbct can model a fan beam CT unit. After reconstruction, the images contained Hounsfield values comparable to measured data.     

Investigation on the resolution of a micro cone beam CT scanner scintillating detector using Monte Carlo methods

The impact of several physical quantities on the spatial resolution of an X-ray scintillating pixel detector for a micro cone beam CT (µCBCT) is investigated and discussed.The XtremeCT from SCANCO Medical AG was simulated using the EGSnrc/EGS++ Monte Carlo (MC) framework and extensively benchmarked in a previous work. The resolution of the detector was determined by simulating a titanium knife-edge to obtain the edge spread function (ESF) and the modulation transfer function (MTF). Propagation of the scintillation light through the scintillator and its coupling into the fiber optics system was taken into account.The contribution of particles scattered in the main scanner components to the detector signal is very low and does not affect the spatial resolution of the detector. The resolution obtained from the energy deposition in the scintillator without any blurring due to the propagation of the scintillation light into the fiber optics array was 31 µm. By assuming isotropic light propagation in the scintillator, the resolution degraded to 360 µm. A simple light propagation model taking into account the impact of the scintillator’s columnar microstructures was developed and compared with the MANTIS Monte Carlo simulation package. By reducing the width of the model’s light propagation kernel by a factor of 2 compared to the isotropic case, the detector resolution can be improved to 83 µm, which corresponds well to the measured resolution of 86 µm.The resolution of the detector is limited mainly by the propagation of the scintillation light through the scintillator layer. It offers the greatest potential to improve the resolution of the µCBCT imaging system.     

Input-output analysis of in vivo photoassimilate translocation using Positron-Emitting Tracer Imaging System (PETIS) data

The Positron-Emitting Tracer Imaging System (PETIS) is introduced for monitoring the distribution of (11)C-labelled photoassimilates in Sorghum. The obtained two-dimensional image data were quantitatively analysed using a transfer function analysis approach. While one half of a Sorghum root in a split root system was treated with either 0, 100, or 500 mM NaCl dissolved in the nutrient solution, tracer images of the root halves and the lower stem section were recorded using PETIS. From the observed tracer levels, parameters were estimated, from which the mean speed of tracer transport and the proportion of tracer moved between specified image positions were deduced. Transport speed varied between 0.7 and 1.8 cm min(-1) with the difference depending on which part of the stem was involved. When data were collected in the lowest 0.5-1 cm of the stem, which included the point where the roots emerge, transport speed was less. Rapid changes in NaCl concentration, from 0 to 100 mM, resulted in short-term increases of assimilate import into the treated root. This response represented a transient osmotic effect, that was compensated for in the medium-term by osmotic adaptation. Higher concentrations of NaCl (500 mM) resulted in distinctly less photoassimilate transport into the treated root half. The present results agree with earlier observations, showing that transport of (11)C-labelled photoassimilates measured with the PETIS detector system can be quantified using the method of input-output analysis. It is worth noting that with the PETIS detector system, areas of interest do not need to be defined until after data collection. This means that unexpected behaviour of a plant organ will be seen, which is not necessarily the case with conventional detector systems looking at predefined areas of interest.     

A GPU Simulation Tool for Training and Optimisation in 2D Digital X-Ray Imaging

Conventional radiology is performed by means of digital detectors, with various types of technology and different performance in terms of efficiency and image quality. Following the arrival of a new digital detector in a radiology department, all the staff involved should adapt the procedure parameters to the properties of the detector, in order to achieve an optimal result in terms of correct diagnostic information and minimum radiation risks for the patient. The aim of this study was to develop and validate a software capable of simulating a digital X-ray imaging system, using graphics processing unit computing. All radiological image components were implemented in this application: an X-ray tube with primary beam, a virtual patient, noise, scatter radiation, a grid and a digital detector. Three different digital detectors (two digital radiography and a computed radiography systems) were implemented. In order to validate the software, we carried out a quantitative comparison of geometrical and anthropomorphic phantom simulated images with those acquired. In terms of average pixel values, the maximum differences were below 15%, while the noise values were in agreement with a maximum difference of 20%. The relative trends of contrast to noise ratio versus beam energy and intensity were well simulated. Total calculation times were below 3 seconds for clinical images with pixel size of actual dimensions less than 0.2 mm. The application proved to be efficient and realistic. Short calculation times and the accuracy of the results obtained make this software a useful tool for training operators and dose optimisation studies.     

MtreeRing: An R package with graphical user interface for automatic measurement of tree ring widths using image processing techniques

Accurate measurements of ring-width series are essential for dendrochronological analyses. We present an R package MtreeRing for ring-width measurements on scanned digital images. A morphological alternate sequential filter is used for noise reduction in the original image. Ring boundaries are determined by the steepest negative slopes in the light reflectance of latewood-earlywood transitions. To automatically identify tree rings, the package provides three alternative methods (watershed-based segmentation, Canny edge detector, and a linear detection algorithm), each with advantages and disadvantages and suited to different wood anatomical features. The user can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. Differences in ring-width measurements between MtreeRing and WinDENDRO in a given coniferous species (Larix gmelinii) were assessed, and no significant difference between programs was found. Furthermore, the package provides an R-based web application which was developed using the Shiny framework. This beginner-friendly application allows viewing and interacting with tree ring images. It requires no programming experience and can run on either a local computer or a remote server.     

Optimal calibration marker mesh for 2D X-ray sensors in 3D reconstruction

Image intensifiers suffer from distortions due to magnetic fields. In order to use this X-ray projections images for computer-assisted medical interventions, image intensifiers need to be calibrated. Opaque markers are often used for the correction of the image distortion and the estimation of the acquisition geometry parameters. Information under the markers is then lost. In this work, we consider the calibration of image intensifiers in the framework of 3D reconstruction from several 2D X-ray projections. In this context, new schemes of marker distributions are proposed for 2D X-ray sensor calibration. They are based on efficient sampling conditions of the parallel-beam X-ray transform when the detector and source trajectory is restricted to a circle around the measured object. Efficient sampling are essentially subset of standard sampling in this situation. The idea is simply to exploit the data redundancy of standard sampling and to replace some holes of efficient schemes by markers. Optimal location of markers in the sparse efficient sampling geometry can thus be found. In this case, the markers can stay on the sensor during the measurement with--theoretically--no loss of information (when the signal-to-noise ratio is large). Even if the theory is based on the parallel-beam X-ray transform, numerical experiments on both simulated and real data are shown in the case of weakly divergent beam geometry. We show that the 3D reconstruction from simulated data with interlaced markers is essentially the same as those obtained from data with no marker. We show that efficient Fourier interpolation formulas based on optimal sparse sampling schemes can be used to recover the information hidden by the markers.     

A new metric for evaluating the correspondence of spatial patterns in vegetation models

Aim  To present a new metric, the 'opposite and identity' (OI) index, for evaluating the correspondence between two sets of simulated time-series dynamics of an ecological variable.
Innovation  The OI index is introduced and its mathematical expression is defined using vectors to denote simulated variations of an ecological variable on the basis of the vector addition rule. The value of the OI index varies from 0 to 1 with a value 0 (or 1) indicating that compared simulations are opposite (or identical). An OI index with a value near 0.5 suggests that the difference in the amplitudes of variations between compared simulations is large. The OI index can be calculated in a grid cell, for a given biome and for time-series simulations. The OI indices calculated in each grid cell can be used to map the spatial agreement between compared simulations, allowing researchers to pinpoint the extent of agreement or disagreement between two simulations. The OI indices calculated for time-series simulations allow researchers to identify the time at which one simulation differs from another. A case study demonstrates the application and reliability of the OI index for comparing two simulated time-series dynamics of terrestrial net primary productivity in Asia from 1982 to 2000. In the case study, the OI index performs better than the correlation coefficient at accurately quantifying the agreement between two simulated time-series dynamics of terrestrial net primary productivity in Asia.
Main conclusions  The OI index provides researchers with a useful tool and multiple flexible ways to compare two simulation results or to evaluate simulation results against observed spatiotemporal data. The OI index can, in some cases, quantify the agreement between compared spatiotemporal data more accurately than the correlation coefficient because of its insensitivity to influential data and outliers and the autocorrelation of simulated spatiotemporal data.     

Precise Cobb Angle Measurement System Based on Spinal Images Merging Function

Background

Convenient and precise measurement of the Cobb angle using a small size X-ray detector has been required for local clinics.

Synchrotron based planar imaging and digital tomosynthesis of breast and biopsy phantoms using a CMOS active pixel sensor

The SYRMEP (SYnchrotron Radiation for MEdical Physics) beamline at Elettra is performing the first mammography study on human patients using free-space propagation phase contrast imaging. The stricter spatial resolution requirements of this method currently force the use of conventional films or specialized computed radiography (CR) systems. This also prevents the implementation of three-dimensional (3D) approaches. This paper explores the use of an X-ray detector based on complementary metal-oxide-semiconductor (CMOS) active pixel sensor (APS) technology as a possible alternative, for acquisitions both in planar and tomosynthesis geometry.Results indicate higher quality of the images acquired with the synchrotron set-up in both geometries. This improvement can be partly ascribed to the use of parallel, collimated and monochromatic synchrotron radiation (resulting in scatter rejection, no penumbra-induced blurring and optimized X-ray energy), and partly to phase contrast effects. Even though the pixel size of the used detector is still too large – and thus suboptimal – for free-space propagation phase contrast imaging, a degree of phase-induced edge enhancement can clearly be observed in the images.     

Dual energy radiography using X-ray films and intensifying screens

The aim of this study was to investigate dual energy (DE) systems using X-ray films and intensifying screens as detecting media. This has been studied using both experimental methods and numerical modelling. Numerical methods were used to calculate energy losses due to K-fluourescent escape originating from the phosphors of the intensifying screens. This enabled the calculation of absorbed energy in screens. The method for screen selection and prediction of performance used the fact that detector response depends upon impinging X-ray energy. By equating the detector's absorbing characteristics to the resultant optical density (OD), an absorbed energy constant was calculated. These constants were used to predict OD for a given X-ray spectrum and hence simulation of detector characteristics. Experimental techniques were used to investigate sensitivity to chemical composition changes. These results compared favourably with computed values. It was demonstrated that although limitations exist, detector simulations are valid and X-ray film intensifying screen combinations make adequate DE detectors.     

Molecular Dynamics Simulations of Molecules in Uniform Flow

Flow at the molecular level induces shear-induced unfolding of single proteins and can drive their assembly, the mechanisms of which are not completely understood. To be able to analyze the role of flow on molecules, we present uniform-flow molecular dynamics simulations at atomic level. The pull module of the GRoningen MAchine for Chemical Simulations package was extended to be able to force-group atoms within a defined layer of the simulation box. Application of this external enforcement to explicit water molecules, together with the coupling to a thermostat, led to a uniform terminal velocity of the solvent water molecules. We monitored the density of the whole system to establish the conditions under which the simulated flow is well-behaved. A maximal velocity of 1.3 m/s can be generated if a pull slice of 8 nm is used, and high velocities would require larger pull slices to still maintain a stable density. As expected, the target velocity increases linearly with the total external force applied. Finally, we suggest an appropriate setup to stretch a protein by uniform flow, in which protein extensions depend on the flow conditions. Our implementation provides an efficient computational tool to investigate the effect of the flow at the molecular level.     

Simulation of scanner- and patient-specific low-dose CT imaging from existing CT images

PurposeSimulating low-dose Computed Tomography (CT) facilitates in-silico studies into the required dose for a diagnostic task. Conventionally, low-dose CT images are created by adding noise to the projection data. However, in practice the raw data is often simply not available. This paper presents a new method for simulating patient-specific, low-dose CT images without the need of the original projection data.MethodsThe low-dose CT simulation method included the following: (1) computation of a virtual sinogram from a high dose CT image through a radon transform; (2) simulation of a ‘reduced’-dose sinogram with appropriate amounts of noise; (3) subtraction of the high-dose virtual sinogram from the reduced-dose sinogram; (4) reconstruction of a noise volume via filtered back-projection; (5) addition of the noise image to the original high-dose image. The required scanner-specific parameters, such as the apodization window, bowtie filter, the X-ray tube output parameter (reflecting the photon flux) and the detector read-out noise, were retrieved from calibration images of a water cylinder. The low-dose simulation method was evaluated by comparing the noise characteristics in simulated images with experimentally acquired data.ResultsThe models used to recover the scanner-specific parameters fitted accurately to the calibration data, and the values of the parameters were comparable to values reported in literature. Finally, the simulated low-dose images accurately reproduced the noise characteristics in experimentally acquired low-dose-volumes.ConclusionThe developed methods truthfully simulate low-dose CT imaging for a specific scanner and reconstruction using filtered backprojection. The scanner-specific parameters can be estimated from calibration data.     

External cross-validation for unbiased evaluation of protein family detectors: application to allergens

Key issues in protein science and computational biology are design and evaluation of algorithms aimed at detection of proteins that belong to a specific family, as defined by structural, evolutionary, or functional criteria. In this context, several validation techniques are often used to compare different parameter settings of the detector, and to subsequently select the setting that yields the smallest error rate estimate. A frequently overlooked problem associated with this approach is that this smallest error rate estimate may have a large optimistic bias. Based on computer simulations, we show that a detector's error rate estimate can be overly optimistic and propose a method to obtain unbiased performance estimates of a detector design procedure. The method is founded on an external 10-fold cross-validation (CV) loop that embeds an internal validation procedure used for parameter selection in detector design. The designed detector generated in each of the 10 iterations are evaluated on held-out examples exclusively available in the external CV iterations. Notably, the average of these 10 performance estimates is not associated with a final detector, but rather with the average performance of the design procedure used. We apply the external CV loop to the particular problem of detecting potentially allergenic proteins, using a previously reported design procedure. Unbiased performance estimates of the allergen detector design procedure are presented together with information about which algorithms and parameter settings that are most frequently selected.     

Issues of resolution and polymorphism in single-particle reconstruction

Three-dimensional reconstruction from electron microscopic (EM) images of isolated macromolecular complexes is being employed by many laboratories. This approach is extremely powerful and continues to improve in resolution. In the absence of stereochemical constraints that can be used to assess the quality of a reconstruction, as exist in X-ray crystallography, several other measures have typically been used. A very useful assessment of quality can be made in the comparison between the projections of the three-dimensional reconstruction and averages generated from classes of images. The main quantitative measure has been that of resolution statistics, typically based upon Fourier shell correlations. We show, using only simulated noise for images, that impressive resolution statistics are generated that can even extend the apparent resolution of the starting model. When truly independent reconstructions are generated starting from different initial models, however, such artefacts are not possible. We also show, using real images of DnaB rings, that in the presence of polymorphism artefactual reconstructions can be generated whose projections match class averages. These averages, however, are themselves artefactual as they involve heterogeneous images. The issues presented here need to be considered when single-particle EM reconstructions are evaluated.     

X-ray scatter data for flat-panel detector CT

In modern X-ray computed tomography (CT) a trend to increased volume coverage by using multi-row detectors is apparent. Flat-panel detector CT (FPD-CT) systems provide an even larger field of measurement which, however, results in an increased scatter fraction. We investigated the scatter intensities registered in the case of FPD-CT. A hybrid model for the simulation of scatter combining deterministic and Monte Carlo methods was used for the scatter calculations. The influence of imaging parameters on the registered scatter intensity was examined both in single projections and reconstructed images. Scatter-to-primary ratios (SPRs) are given for various values of object thickness, field size, object-to-detector distance, incident energy and projection angle. For the simulations, homogeneous water phantoms and realistic patient data sets were used to produce scatter data representative for clinical situations. The SPR increases with object size, collimation and z-extent resulting in SPR ≫ 1 and respective scatter artifacts in the reconstructed images. In contrary, the scatter intensity decreases non-linearly with the object-to-detector distance. The angular and spatial distributions of scatter form a flat function as compared to the distribution of the primary signal. Single scatter appears to determine the distribution and magnitude of the total-scatter intensity at the detector.     

A direct Fourier method (DFM) for X-ray tomographic reconstructions and the accurate simulation of sinograms

This article illustrates the reconstruction of tomographic images by a direct Fourier method (DFM) and the results obtained from simulations and from experimental X-ray sinograms. The implementation of DFM, especially with regard to the resampling of the 2D Fourier transform, is based on a technique of Shannon reconstruction, devised by the authors, and on novel interpolating kernels. A short account is given on the principles and the implementation aspects of the interpolation technique. The DFM protocol developed by the authors has been tested, both for parallel and fan geometry, on simulated sinograms obtained from real images and from phantoms. The technique used to compute accurate projections is also described, since it might be useful in restoring missing parts of sinograms with processes based on ‘projections on convex sets’ (POCS) techniques. The results obtained from simulations and from the raw data of a third generation tomograph are presented and discussed. A comparison among reconstructions obtained from complete sinograms and from half of them suggests that adequate images could be obtained with a radiation dose lower than that used to obtain the experimental sinograms.     

Simulator for migration processes and wear in the artificial hip acetabulum for radiologic measurement]

For assessing migration of cups, standard X-rays or stereo radiological images (SRI) are available. In addition, software is also available for measurements. The accuracies of the various systems are established statistically, in part combined with phantoms, and compared. To date, no known phantom is available for the simulation of acetabular cup migration with account being taken of the position of the pelvis in the X-ray beam. Such an appliance covering 8 different parameters has now been developed, the cup can be moved horizontally, vertically and in the loading direction. Angular accuracy is +/- 0.5 degree, and wear of a magnitude of 0.25 mm can be simulated. Two degree elevation of the pelvis, left or right, can be simulated. The position of the pelvis around the horizontal axis permits continuous variation. This appliance can simulate migratory movements of the acetabular cup within a pelvis, and wear within the cup. In addition, the spatial position of the pelvis can be varied. The X-ray images can be used to investigate the accuracy of evaluation strategies.     

Combination of Neutron Scattering and Molecular Dynamics to Determine Internal Motions in Biomolecules

Abstract

The forms and frequencies of atomic dynamics on the pico- and nanosecond timescales are accessible experimentally using incoherent neutron scattering. Molecular dynamics simulations cover the same space and time domains and neutron scattering intensities can be calculated from the simulations for direct comparison with experiment. To illustrate the complementarity of neutron scattering and molecular dynamics we examine measured and simulation-derived elastic incoherent scattering profiles from myoglobin and from the crystalline alanine dipeptide. Elastic incoherent scattering gives information on the geometry of the volume accessible to the atoms in the samples. The simulation-derived dipeptide elastic scattering profiles are in reasonable accord with experiment, deviations being due to the sampling limitations in the simulations and experimental detector normalisation procedures. The simulated dynamics is decomposed, revealing characteristic profiles due to rotational diffusional and translational vibrational motions of the methyl groups. In myoglobin, for which the timescale of the simulation matches more closely that accessible to the experiment, good agreement is seen for the elastic incoherent structure factor. This indicates that the space sampled by the hydrogen atoms in the protein on the timescale <100 ps is well represented by the simulation. Part of the helix atom fluctuations can be described in terms of rigid helix motions.