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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Modularization of EDGE Workflows Using Nextflow: Improving the Efficiency and Maintainability of Bioinformatics Software

EDGE is a bioinformatics platform developed in 2016 by researchers at Los Alamos National Laboratory (LANL) to facilitate the analysis of next-generation sequencing data by researchers with varying levels of experience in bioinformatics (Li et al., 2017). Users with single-end, paired-end or long-read sequencing data can provide their reads as input to EDGE and select the combination of workflows to run that are most useful for their research (e.g., quality control of reads, genome assembly, or the taxonomic classification of input reads). Table 1 summarizes the modules available in EDGE. EDGE is available as a web platform at https://edgebioinformatics.org, as installable source code maintained on GitHub under a GPLv3 license, and as a publicly hosted Docker image.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Classification of multispectral or hyperspectral satellite imagery using clustering of sparse approximations on sparse representations in learned dictionaries obtained using efficient convolutional sparse coding

An approach for land cover classification, seasonal and yearly change detection and monitoring, and identification of changes in man-made features may use a clustering of sparse approximations (CoSA) on sparse representations in learned dictionaries. The learned dictionaries may be derived using efficient convolutional sparse coding to build multispectral or hyperspectral, multiresolution dictionaries that are adapted to regional satellite image data. Sparse image representations of images over the learned dictionaries may be used to perform unsupervised k-means clustering into land cover categories. The clustering process behaves as a classifier in detecting real variability. This approach may combine spectral and spatial textural characteristics to detect geologic, vegetative, hydrologic, and man-made features, as well as changes in these features over time.

47 OTHER INSTRUMENTATION↗
DOE OSTI2013

THE 0.5-2.22 {mu}m SCATTERED LIGHT SPECTRUM OF THE DISK AROUND TW Hya: DETECTION OF A PARTIALLY FILLED DISK GAP AT 80 AU

We present a 0.5-2.2 {mu}m scattered light spectrum of the circumstellar disk around TW Hya from a combination of spatially resolved Hubble Space Telescope STIS spectroscopy and NICMOS coronagraphic images of the disk. We investigate the morphology of the disk at distances >40 AU over this wide range of wavelengths, and identify the presence of a depression in surface brightness at {approx}80 AU that could be caused by a gap in the disk. Additionally, we quantify the surface brightness, azimuthal symmetry, and spectral character of the disk as a function of radius. Our analysis shows that the scattering efficiency of the dust is largely neutral to blue over the observed wavelengths. We model the disk as a steady {alpha}-disk with an ad hoc gap structure. The thermal properties of the disk are self-consistently calculated using a three-dimensional radiative transfer code that uses ray tracing to model the heating of the disk interior and scattered light images. We find a good fit to the data over a wide range of distances from the star if we use a model disk with a partially filled gap of 30% depth at 80 AU and with a self-similar truncation knee at 100 AU. The origin of the gap is unclear, but it could arise from a transition in the nature of the disk's dust composition or the presence of a planetary companion. Based on scalings to previous hydrodynamic simulations of gap-opening criteria for embedded proto-planets, we estimate that a planetary companion forming the gap could have a mass between 6 and 28 M{sub Circled-Plus }.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

TIA: A forward model and analyzer for Talbot interferometry experiments of dense plasmas

Interferometry is one of the most sensitive and successful diagnostic methods for plasmas. However, owing to the design of most common interferometric systems, the wavelengths of operation and, therefore, the range of densities and temperatures that can be probed are severely limited. Talbot–Lau interferometry offers the possibility of extending interferometry measurements to x-ray wavelengths by means of the Talbot effect. While there have been several proof-of-concept experiments showing the efficacy of this method, it is only recently that experiments to probe High Energy Density (HED) plasmas using Talbot–Lau interferometry are starting to take place. To improve these experimental designs, we present here the Talbot-Interferometry Analyzer (TIA) tool, a forward model for generating and postprocessing synthetic x-ray interferometry images from a Talbot–Lau interferometer. Although TIA can work with any two-dimensional hydrodynamic code to study plasma conditions as close to reality as possible, this software has been designed to work by default with output files from the hydrodynamic code FLASH, making the tool user-friendly and accessible to the general plasma physics community. Here, the model has been built into a standalone app, which can be installed by anyone with access to the MATLAB runtime installer and is available upon request to the authors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Analyzed DTS Data, Guelph, ON Canada

Analyzed DTS datasets from active heat injection experiments in Guelph, ON Canada is included. A .pdf file of images including borehole temperature distributions, temperature difference distributions, temperature profiles, and flow interpretations is included as the primary analyzed dataset. Analyzed data used to create the .pdf images are included as a matlab data file that contains the following 5 types of data: 1) Borehole Temperature (matrix of temperature data collected in the borehole), 2) Borehole Temperature Difference (matrix of temperature difference above ambient for each test), 3) Borehole Time (time in both min and sec since the start of a DTS test), 4) Borehole Depth (channel depth locations for the DTS measurements), 5) Temperature Profiles (ambient, active, active off early time, active off late time, and injection).

15 GEOTHERMAL ENERGY↗
DOE OSTI2012

Measurements of ion cyclotron range of frequencies mode converted wave intensity with phase contrast imaging in Alcator C-Mod and comparison with full-wave simulations

Radio frequency waves in the ion cyclotron range of frequencies (ICRF) are widely used to heat tokamak plasmas. In ICRF heating schemes involving multiple ion species, the launched fast waves convert to ion cyclotron waves or ion Bernstein waves at the two-ion hybrid resonances. Mode converted waves are of interest as actuators to optimise plasma performance through current drive and flow drive. In order to describe these processes accurately in a realistic tokamak geometry, numerical simulations are essential, and it is important that these codes be validated against experiment. In this study, the mode converted waves were measured using a phase contrast imaging technique in D-H and D-{sup 3}He plasmas. The measured mode converted wave intensity in the D-{sup 3}He mode conversion regime was found to be a factor of {approx}50 weaker than the full-wave predictions. The discrepancy was reduced in the hydrogen minority heating regime, where mode conversion is weaker.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

SU-E-T-285: Dose Variation at Bone in Small-Animal Irradiation: A Monte Carlo Study Using Monoenergetic Photon Beams

Purpose: The aim of this study is to investigate the variation of bone dose on photon beam energy (keV – MeV) in small-animal irradiation. Dosimetry of homogeneous and inhomogeneous phantoms as per the same mouse computed tomography image set were calculated using the DOSCTP and DOSXYZnrc based on the EGSnrc Monte Carlo code. Methods: Monte Carlo simulations for the homogeneous and inhomogeneous mouse phantom irradiated by a 360 degree photon arc were carried out. Mean doses of the bone tissue in the irradiated volumes were calculated at various photon beam energies, ranging from 50 keV to 1.25 MeV. The effect of bone inhomogeneity was examined through the Inhomogeneous Correction Factor (ICF), a dose ratio of the inhomogeneous to the homogeneous medium. Results: From our Monte Carlo results, higher mean bone dose and ICF were found when using kilovoltage photon beams compared to megavoltage. In beam energies ranging from 50 keV to 200 keV, the bone dose was found maximum at 50 keV, and decreased significantly from 2.6 Gy to 0.55 Gy, when 2 Gy was delivered at the center of the phantom (isocenter). Similarly, the ICF were found decreasing from 4.5 to 1 when the photon beam energy was increased from 50 keV to 200 keV. Both mean bone dose and ICF remained at about 0.5 Gy and 1 from 200 keV to 1.25 MeV with insignificant variation, respectively. Conclusion: It is concluded that to avoid high bone dose in the small-animal irradiation, photon beam energy higher than 200 keV should be used with the ICF close to one, and bone dose comparable to the megavoltage beam where photoelectric effect is not dominant.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Synthetic-aperture radar (SAR) imaging with range-resolved reflection data

SAR imaging may be performed with range-resolved reflection data, where a spread-spectrum signal, such as a code division multiple access (CDMA) signal, is transmitted instead of a simple frequency chirp. The reflected spread-spectrum signal may be analyzed to gather range-resolved reflection data. Range-resolved reflection data may be gathered at each angular view. This data may be used to construct a more accurate approximation of the Fourier transform of the desired image than can be done by a conventional SAR approach. The image may be reconstructed from this Fourier transform using Fourier inversion techniques similar to those used in conventional SAR approaches. The range-resolved reflection scheme generally requires somewhat more processing to recover the image as compared with conventional SAR systems, but provides a significantly more stable image with less degradation from effects that plague conventional SAR systems. This can eliminate the need for phase coherency altogether and also eliminate “phase drift,” which leads to image distortion. This may be especially well suited for high resolution imaging of relatively large targets.

47 OTHER INSTRUMENTATION↗
DOE OSTI2012

Plate-specific gain map correction for the improvement of detective quantum efficiency in computed radiography

Purpose: The purpose of this work is to improve the noise power spectrum (NPS), and thus the detective quantum efficiency (DQE), of computed radiography (CR) images by correcting for spatial gain variations specific to individual imaging plates. CR devices have not traditionally employed gain-map corrections, unlike the case with flat-panel detectors, because of the multiplicity of plates used with each reader. The lack of gain-map correction has limited the DQE(f) at higher exposures with CR. This current work describes a feasible solution to generating plate-specific gain maps. Methods: Ten high-exposure open field images were taken with an RQA5 spectrum, using a sixth generation CR plate suspended in air without a cassette. Image values were converted to exposure, the plates registered using fiducial dots on the plate, the ten images averaged, and then high-pass filtered to remove low frequency contributions from field inhomogeneity. A gain-map was then produced by converting all pixel values in the average into fractions with mean of one. The resultant gain-map of the plate was used to normalize subsequent single images to correct for spatial gain fluctuation. To validate performance, the normalized NPS (NNPS) for all images was calculated both with and without the gain-map correction. Variations in the quality of correction due to exposure levels, beam voltage/spectrum, CR reader used, and registration were investigated. Results: The NNPS with plate-specific gain-map correction showed improvement over the noncorrected case over the range of frequencies from 0.15 to 2.5 mm{sup -1}. At high exposure (40 mR), NNPS was 50%-90% better with gain-map correction than without. A small further improvement in NNPS was seen from carefully registering the gain-map with subsequent images using small fiducial dots, because of slight misregistration during scanning. Further improvement was seen in the NNPS from scaling the gain map about the mean to account for different beam spectra. Conclusions: This study demonstrates that a simple gain-map can be used to correct for the fixed-pattern noise in a given plate and thus improve the DQE of CR imaging. Such a method could easily be implemented by manufacturers because each plate has a unique bar code and the gain-map for all plates associated with a reader could be stored for future retrieval. These experiments indicated that an improvement in NPS (and hence, DQE) is possible, depending on exposure level, over a wide range of frequencies with this technique.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2025

Multiscale aperture synthesis imager

Synthetic aperture imaging has enabled breakthrough observations from radar to astronomy. However, optical implementation remains challenging due to stringent wavefield synchronization requirements among multiple receivers. Here we present the multiscale aperture synthesis imager (MASI), which utilizes parallelism to break complex optical challenges into tractable sub-problems. MASI employs a distributed array of coded sensors that operate independently yet coherently to surpass the diffraction limit of single receiver. It combines the propagated wavefields from individual sensors through a computational phase synchronization scheme, eliminating the need for overlapping measurement regions to establish phase coherence. Light diffraction in MASI naturally expands the imaging field, generating phase-contrast visualizations that are substantially larger than sensor dimensions. Without using lenses, MASI resolves sub-micron features at ultralong working distances and reconstructs 3D shapes over centimeter-scale fields. MASI transforms the intractable optical synchronization problem into a computational one, enabling practical deployment of scalable synthetic aperture systems at optical wavelengths.

electrical and electronic engineering↗
DOE OSTI2014

SU-E-J-203: Reconstruction of the Treatment Area by Use of Sinogram in Helical Tomotherapy

Purpose: TomoTherapy (Accuray Co.) has an image-guided radiotherapy system with megavoltage (MV) X-ray source and the on-board imaging device. With the MV computed tomography (MVCT), it became feasible to perform the efficient daily-3D registration of the patient position before each treatment delivery. This system also allows one to acquire the delivery sinogram during the actual treatment, which partly includes the information of the irradiated object. In this study, we try to develop the image reconstruction during treatment in helical Tomotherapy. Methods: Sinogram data were acquired during helical Tomotherapy delivery using an arc-shaped detector array that consists of 738 xenon-gas filled detector cells. In preprocessing, these were normalized by full air-scan data. A software program was developed that reconstructs 3D images during treatment with corrections as; (1) the regions outside the field were masked not to be added in the backprojection (a masking correction), and (2) each voxel of the reconstructed image was divided by the number of the X-ray passing through its voxel (a ray-passing correction). Results: Without masking and ray-passing corrections, the image reconstruction was failed. The masking correction made the image clear, however, the streak artifact was accompanied. The ray-passing correction reduced this artifact. Although the SNR (the ratio of mean to standard deviation in homogeneous region) and the contrast of the reconstructed image were slightly improved with the ray-passing correction, the masking correction only is enough for the visualization purpose. Conclusion: The visualization of the treatment area was feasible by use of the sinogram in helical Tomotherapy. This proposed method can be utilized in the treatment verification. This work was partly supported by JSPS KAKENHI 24234567. No COI, but the data in this paper were prepared by collaborators in Accuray.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

BrachyView: Proof-of-principle of a novel in-body gamma camera for low dose-rate prostate brachytherapy

Purpose: The conformity of the achieved dose distribution to the treatment plan strongly correlates with the accuracy of seed implantation in a prostate brachytherapy treatment procedure. Incorrect seed placement leads to both short and long term complications, including urethral and rectal toxicity. The authors present BrachyView, a novel concept of a fast intraoperative treatment planning system, to provide real-time seed placement information based on in-body gamma camera data. BrachyView combines the high spatial resolution of a pixellated silicon detector (Medipix2) with the volumetric information acquired by a transrectal ultrasound (TRUS). The two systems will be embedded in the same probe so as to provide anatomically correct seed positions for intraoperative planning and postimplant dosimetry. Dosimetric calculations are based on the TG-43 method using the real position of the seeds. The purpose of this paper is to demonstrate the feasibility of BrachyView using the Medipix2 pixel detector and a pinhole collimator to reconstruct the real-time 3D position of low dose-rate brachytherapy seeds in a phantom. Methods: BrachyView incorporates three Medipix2 detectors coupled to a multipinhole collimator. Three-dimensionally triangulated seed positions from multiple planar images are used to determine the seed placement in a PMMA prostate phantom in real time. MATLAB codes were used to test the reconstruction method and to optimize the device geometry. Results: The results presented in this paper show a 3D position reconstruction accuracy of the seed in the range of 0.5-3 mm for a 10-60 mm seed-to-detector distance interval (Z direction), respectively. The BrachyView system also demonstrates a spatial resolution of 0.25 mm in the XY plane for sources at 10 mm distance from Medipix2 detector plane, comparable to the theoretical value calculated for an equivalent gamma camera arrangement. The authors successfully demonstrated the capability of BrachyView for real-time imaging (using a 3 s data acquisition time) of different brachytherapy seed configurations (with an activity of 0.05 U) throughout a 60 Multiplication-Sign 60 Multiplication-Sign 60 mm{sup 3} Perspex prostate phantom. Conclusions: The newly developed miniature gamma camera component of BrachyView, with its high spatial resolution and real time capability, allows accurate 3D localization of seeds in a prostate phantom. Combination of the gamma camera with TRUS in a single probe will complete the BrachyView system.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Nonrigid registration-based coronary artery motion correction for cardiac computed tomography

Purpose: X-ray computed tomography angiography (CTA) is the modality of choice to noninvasively monitor and diagnose heart disease with coronary artery health and stenosis detection being of particular interest. Reliable, clinically relevant coronary artery imaging mandates high spatiotemporal resolution. However, advances in intrinsic scanner spatial resolution (CT scanners are available which combine nearly 900 detector columns with focal spot oversampling) can be tempered by motion blurring, particularly in patients with unstable heartbeats. As a result, recently numerous methods have been devised to improve coronary CTA imaging. Solutions involving hardware, multisector algorithms, or {beta}-blockers are limited by cost, oversimplifying assumptions about cardiac motion, and populations showing contraindications to drugs, respectively. This work introduces an inexpensive algorithmic solution that retrospectively improves the temporal resolution of coronary CTA without significantly affecting spatial resolution. Methods: Given the goal of ruling out coronary stenosis, the method focuses on 'deblurring' the coronary arteries. The approach makes no assumptions about cardiac motion, can be used on exams acquired at high heart rates (even over 75 beats/min), and draws on a fast and accurate three-dimensional (3D) nonrigid bidirectional labeled point matching approach to estimate the trajectories of the coronary arteries during image acquisition. Motion compensation is achieved by employing a 3D warping of a series of partial reconstructions based on the estimated motion fields. Each of these partial reconstructions is created from data acquired over a short time interval. For brevity, the algorithm 'Subphasic Warp and Add' (SWA) reconstruction. Results: The performance of the new motion estimation-compensation approach was evaluated by a systematic observer study conducted using nine human cardiac CTA exams acquired over a range of average heart rates between 68 and 86 beats/min. Algorithm performance was based-lined against exams reconstructed using standard filtered-backprojection (FBP). The study was performed by three experienced reviewers using the American Heart Association's 15-segment model. All vessel segments were evaluated to quantify their viability to allow a clinical diagnosis before and after motion estimation-compensation using SWA. To the best of the authors' knowledge this is the first such observer study to show that an image processing-based software approach can improve the clinical diagnostic value of CTA for coronary artery evaluation. Conclusions: Results from the observer study show that the SWA method described here can dramatically reduce coronary artery motion and preserve real pathology, without affecting spatial resolution. In particular, the method successfully mitigated motion artifacts in 75% of all initially nondiagnostic coronary artery segments, and in over 45% of the cases this improvement was enough to make a previously nondiagnostic vessel segment clinically diagnostic.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Three dosimetry models of lipoma arborescens treated by {sup 90}Y synovectomy

Purpose: Lipoma arborescens (LA) is a benign intra-articular lipomatous proliferation of the synovial membrane. This extremely rare condition has previously been treated by intra-articular{sup 90}Y radiosynoviorthesis but dosimetry literature on this form of radionuclide therapy is nonexistent. The authors detail methodology for successful treatment of LA and provide for the first time estimates of radiation dosimetry. The authors also analyze the biodistribution of the radiopharmaceutical over the course of the patient's treatment through sequential imaging. Methods: A patient with bilateral LA underwent intracavity injection of{sup 90}Y citrate colloid to the right and left knee joint spaces (181 and 198 MBq, respectively). SPECT/CT datasets were acquired over 9 days to quantify the biodistribution and kinetics of the radiopharmaceutical. Radiation dosimetry was performed using the MIRD schema (through OLINDA software), a custom voxel-based method, and a direct Monte Carlo calculation (OEDIPE). Results: Follow-up MRI showed marked reduction in LA size in both knees. Mean absorbed doses to the LA were 21.2 ± 0.8 and 42.9 ± 2.3 Gy using OLINDA, 8.1 ± 0.3 and 16.7 ± 0.5 Gy using voxel based methodology, and 8.2 ± 0.3 and 15.7 ± 0.5 Gy for OEDIPE in the right and left LA, respectively. Distribution of the radiopharmaceutical within the joint space alters over the imaging period, with less than 1% of the remaining activity having moved posteriorly in the knee cavity. No uptake was detected outside of the joint space after assessment with whole-body scintigraphy. Conclusions: An activity of approximately 185 MBq successfully relieved clinical symptoms of LA. There was good correlation between direct Monte Carlo and voxel based techniques, but OLINDA was shown to overestimate the absorbed dose to the tumor. Accurate dosimetry may help select an activity more tailored to the specific size and location of the LA.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2012

4D cone beam CT via spatiotemporal tensor framelet

Purpose: On-board 4D cone beam CT (4DCBCT) offers respiratory phase-resolved volumetric imaging, and improves the accuracy of target localization in image guided radiation therapy. However, the clinical utility of this technique has been greatly impeded by its degraded image quality, prolonged imaging time, and increased imaging dose. The purpose of this letter is to develop a novel iterative 4DCBCT reconstruction method for improved image quality, increased imaging speed, and reduced imaging dose. Methods: The essence of this work is to introduce the spatiotemporal tensor framelet (STF), a high-dimensional tensor generalization of the 1D framelet for 4DCBCT, to effectively take into account of highly correlated and redundant features of the patient anatomy during respiration, in a multilevel fashion with multibasis sparsifying transform. The STF-based algorithm is implemented on a GPU platform for improved computational efficiency. To evaluate the method, 4DCBCT full-fan scans were acquired within 30 s, with a gantry rotation of 200°; STF is also compared with a state-of-art reconstruction method via spatiotemporal total variation regularization. Results: Both the simulation and experimental results demonstrate that STF-based reconstruction achieved superior image quality. The reconstruction of 20 respiratory phases took less than 10 min on an NVIDIA Tesla C2070 GPU card. The STF codes are available at https://sites.google.com/site/spatiotemporaltensorframelet . Conclusions: By effectively utilizing the spatiotemporal coherence of the patient anatomy among different respiratory phases in a multilevel fashion with multibasis sparsifying transform, the proposed STF method potentially enables fast and low-dose 4DCBCT with improved image quality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Poster - 40: Treatment Verification of a 3D-printed Eye Phantom for Proton Therapy

Purpose: Ocular melanoma is a form of eye cancer which is often treated using proton therapy. The benefit of the steep proton dose gradient can only be leveraged for accurate patient eye alignment. A treatment-planning program was written to plan on a 3D-printed anatomical eye-phantom, which was then irradiated to demonstrate the feasibility of verifying in vivo dosimetry for proton therapy using PET imaging. Methods: A 3D CAD eye model with critical organs was designed and voxelized into the Monte-Carlo transport code FLUKA. Proton dose and PET isotope production were simulated for a treatment plan of a test tumour, generated by a 2D treatment-planning program developed using NumPy and proton range tables. Next, a plastic eye-phantom was 3D-printed from the CAD model, irradiated at the TRIUMF Proton Therapy facility, and imaged using a PET scanner. Results: The treatment-planning program prediction of the range setting and modulator wheel was verified in FLUKA to treat the tumour with at least 90% dose coverage for both tissue and plastic. An axial isotope distribution of the PET isotopes was simulated in FLUKA and converted to PET scan counts. Meanwhile, the 3D-printed eye-phantom successfully yielded a PET signal. Conclusions: The 2D treatment-planning program can predict required parameters to sufficiently treat an eye tumour, which was experimentally verified using commercial 3D-printing hardware to manufacture eye-phantoms. Comparison between the simulated and measured PET isotope distribution could provide a more realistic test of eye alignment, and a variation of the method using radiographic film is being developed.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

High speed two-dimensional imaging with an analog interface

A quantitative pulse count (event detection) algorithm with linearity to high count rates is accomplished by combining a high-speed, high frame rate camera with simple logic code run on a massively parallel processor such as a GPU. The parallel processor elements examine frames from the camera pixel by pixel to find and tag events or count pulses. The tagged events are combined to form a combined quantitative event image.

Waugh, Justin↗