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Evaporation from the soil surface (E) can be a significant source of water loss in arid areas. In sparsely vegetated systems, E is expected to be a function of soil, climate, irrigation regime, precipitation patterns, and plant canopy development and will therefore change dynamically at both daily and seasonal time scales. The objectives of this research were to quantify E in an isolated, drip-irrigated vineyard in an arid environment and to simulate below canopy E using the HYDRUS (2-D/3-D) model. Specific focus was on variations of E both temporally and spatially across the inter-row. Continuous above canopy measurements, made in a commercial vineyard, included evapotranspiration, solar radiation, air temperature and humidity, and wind speed and direction. Short-term intensive measurements below the canopy included actual and potential E and solar radiation along transects between adjacent vine-rows. Potential and actual E below the canopy were highly variable, both diurnally and with distance from the vine-row, as a result of shading and distinct wetted areas typical to drip irrigation. While the magnitude of actual E was mostly determined by soil water content, diurnal patterns depended strongly on position relative to the vine-row due to variable shading patterns. HYDRUS (2-D/3-D) successfully simulated the magnitude, diurnal patterns, and spatial distribution of E, including expected deviations as a result of variability in soil saturated hydraulic conductivity. © 2014. American Geophysical Union.

Background: As a leading cause of death, worldwide, cardiovascular disease is of great clinical importance. Among cardiovascular diseases, coronary artery disease (CAD) is a key contributor, and it is the attributed cause of death for 10% of all deaths annually. The prevalence of CAD is commensurate with the rise in new medical imaging technologies intended to aid in its diagnosis and treatment. The necessary clinical trials required to validate and optimize these technologies require a large cohort of carefully controlled patients, considerable time to complete, and can be prohibitively expensive. A safer, faster, less expensive alternative is using virtual imaging trials (VITs), utilizing virtual patients or phantoms combined with accurate computer models of imaging devices., Purpose: In this work, we develop realistic, physiologically-informed models for coronary plaques for application in cardiac imaging VITs., Methods: Histology images of plaques at micron-level resolution were used to train a deep convolutional generative adversarial network (DC-GAN) to create a library of anatomically variable plaque models with clinical anatomical realism. The stability of each plaque was evaluated by finite element analysis (FEA) in which plaque components and vessels were meshed as volumes, modeled as specialized tissues, and subjected to the range of normal coronary blood pressures. To demonstrate the utility of the plaque models, we combined them with the whole-body XCAT computational phantom to perform initial simulations comparing standard energy-integrating detector (EID) CT with photon-counting detector (PCD) CT., Results: Our results show the network is capable of generating realistic, anatomically variable plaques. Our simulation results provide an initial demonstration of the utility of the generated plaque models as targets to compare different imaging devices., Conclusions: Vast, realistic, and variable CAD pathologies can be generated to incorporate into computational phantoms for VITs. There they can serve as a known truth from which to optimize and evaluate cardiac imaging technologies quantitatively., (© 2024 American Association of Physicists in Medicine.)

Objective. Virtual imaging trials enable efficient assessment and optimization of medical image devices and techniques via simulation rather than physical studies. These studies require realistic, detailed ground-truth models or phantoms of the relevant anatomy or physiology. Anatomical structures within computational phantoms are typically based on medical imaging data; however, for small and intricate structures (e.g. trabecular bone), it is not reasonable to use existing clinical data as the spatial resolution of the scans is insufficient. In this study, we develop a mathematical method to generate arbitrary-resolution bone structures within virtual patient models (XCAT phantoms) to model the appearance of CT-imaged trabecular bone. Approach . Given surface definitions of a bone, an algorithm was implemented to generate stochastic bicontinuous microstructures to form a network to define the trabecular bone structure with geometric and topological properties indicative of the bone. For an example adult male XCAT phantom (50th percentile in height and weight), the method was used to generate the trabecular structure of 46 chest bones. The produced models were validated in comparison with published properties of bones. The utility of the method was demonstrated with pilot CT and photon-counting CT simulations performed using the accurate DukeSim CT simulator on the XCAT phantom containing the detailed bone models. Main results . The method successfully generated the inner trabecular structure for the different bones of the chest, having quantiative measures similar to published values. The pilot simulations showed the ability of photon-counting CT to better resolve the trabecular detail emphasizing the necessity for high-resolution bone models. Significance. As demonstrated, the developed tools have great potential to provide ground truth simulations to access the ability of existing and emerging CT imaging technology to provide quantitative information about bone structures., (© 2023 Institute of Physics and Engineering in Medicine.)

Purpose: Computational abnormalities (e.g., lesion models) for use in medical imaging simulation studies are frequently generated using data collected from clinical images. Although this approach allows for highly-customizable lesion detectability studies on clinical computed tomography (CT) data, the ground-truth lesion models produced with this method do not provide a sufficiently realistic lesion morphology for use with current anthropomorphic simulation studies. This work is intended to demonstrate that the new anatomically-informed lesion model presented here is not inferior to the previous lesion model under CT imaging, and can therefore provide a more biologically-informed model for use with simulated CT imaging studies., Methods: The lesion model was simulated initially from a seed cell with 10 μm diameter placed in an anatomical location within segmented lung CT and was allowed to reproduce locally within the available solid angle in discrete time-intervals (corresponding to synchronous cell cycles) up to a size of ∼200 μm in diameter. Daughter cells of generation G were allowed also to reproduce on the next available time-step given sufficient space. At lesion sizes beyond 200 μm in diameter, the health of subregions of cells were tracked with a Markov chain technique, indicating which regions were likely to continue growing, which were likely stable, and which were likely to develop necrosis given their proximity to anatomical features and other lesion cells. For lesion sizes beyond 500 μm, the lesion was represented with three nested, triangulated surfaces (corresponding to proliferating, dormant, and necrotic regions), indicating how discrete volumes of the lesion were behaving at a particular time. Lesions were then assigned smoothly-varying material properties based on their cellular level health in each region, resulting in a multi-material lesion model. The lesions produced with this model were then voxelized and placed into lung CT images for comparison with both prior work and clinical data. This model was subject to an observer study in which cardiothoracic imaging radiologists assessed the realism of both clinical and synthetic lesions in CT images., Results: The useable outputs of this work were voxel- or surface-based, validated, computational lesions, at a scale clearly visible on clinical CT (3-4 cm). Analysis of the observer study results indicated that the computationally-generated lesions were indistinguishable from clinical lesions (AUC = 0.49, 95% CI = [0.36, 0.61]) and non-inferior to an earlier image-based lesion model-indicating the advantage of the model for use in both hybrid CT images and in simulated CT imaging of the lungs., Conclusions: Results indicated the non-inferiority of this model as compared to previous methods, indicating the utility of the model for use in both hybrid CT images and in simulated CT imaging., (© 2023 American Association of Physicists in Medicine.)

Photon-counting CT (PCCT) is an emerging imaging technology with potential improvements in quantification and rendition of micro-structures due to its smaller detector sizes. The aim of this study was to assess the performance of a new PCCT scanner (NAEOTOM Alpha, Siemens) in quantifying clinically relevant bone imaging biomarkers for characterization of common bone diseases. We evaluated the ability of PCCT in quantifying microarchitecture in bones compared to conventional energy-integrating CT. The quantifications were done through virtual imaging trials, using a 50 percentile BMI male virtual patient, with a detailed model of trabecular bone with varied bone densities in the lumbar spine. The virtual patient was imaged using a validated CT simulator (DukeSim) at CTDI vol of 20 and 40 mGy for three scan modes: ultra-high-resolution PCCT (UHR-PCCT), high-resolution PCCT (HR-PCCT), and a conventional energy-integrating CT (EICT) (FORCE, Siemens). Further, each scan mode was reconstructed with varying parameters to evaluate their effect on quantification. Bone mineral density (BMD), trabecular volume to total bone volume (BV/TV), and radiomics texture features were calculated in each vertebra. The most accurate BMD measurements relative to the ground truth were UHR-PCCT images (error: 3.3% ± 1.5%), compared to HR-PCCT (error: 5.3% ± 2.0%) and EICT (error: 7.1% ± 2.0%). UHR-PCCT images outperformed EICT and HR-PCCT. In BV/TV quantifications, UHR-PCCT (errors of 29.7% ± 11.8%) outperformed HR-PCCT (error: 80.6% ± 31.4%) and EICT (error: 67.3% ± 64.3). UHR-PCCT and HR-PCCT texture features were sensitive to anatomical changes using the sharpest kernel. Conversely, the texture radiomics showed no clear trend to reflect the progression of the disease in EICT. This study demonstrated the potential utility of PCCT technology in improved performance of bone quantifications leading to more accurate characterization of bone diseases.

Purpose: Virtual (in silico) imaging trials (VITs), involving computerized phantoms and models of the imaging process, provide a modern alternative to clinical imaging trials. VITs are faster, safer, and enable otherwise-impossible investigations. Current phantoms used in VITs are limited in their ability to model functional behavior such as contrast perfusion which is an important determinant of dose and image quality in CT imaging. In our prior work with the XCAT computational phantoms, we determined and modeled inter-organ (organ to organ) intravenous contrast concentration as a function of time from injection. However, intra-organ concentration, heterogeneous distribution within a given organ, was not pursued. We extend our methods in this work to model intra-organ concentration within the XCAT phantom with a specific focus on the liver., Methods: Intra-organ contrast perfusion depends on the organ's vessel network. We modeled the intricate vascular structures of the liver, informed by empirical and theoretical observations of anatomy and physiology. The developed vessel generation algorithm modeled a dual-input-single-output vascular network as a series of bifurcating surfaces to optimally deliver flow within the bounding surface of a given XCAT liver. Using this network, contrast perfusion was simulated within voxelized versions of the phantom by using knowledge of the blood velocities in each vascular structure, vessel diameters and length, and the time since the contrast entered the hepatic artery. The utility of the enhanced phantom was demonstrated through a simulation study with the phantom voxelized prior to CT simulation with the relevant liver vasculature prepared to represent blood and iodinated contrast media. The spatial extent of the blood-contrast mixture was compared to clinical data., Results: The vascular structures of the liver were generated with size and orientation which resulted in minimal energy expenditure required to maintain blood flow. Intravenous contrast was simulated as having known concentration and known total volume in the liver as calibrated from time-concentration curves. Measurements of simulated CT ROIs were found to agree with clinically observed values of early arterial phase contrast enhancement of the parenchyma ( ∼ 5 $ \sim 5$ HU). Similarly, early enhancement in the hepatic artery was found to agree with average clinical enhancement ( 180 $(180$ HU)., Conclusions: The computational methods presented here furthered the development of the XCAT phantoms allowing for multi-timepoint contrast perfusion simulations, enabling more anthropomorphic virtual clinical trials intended for optimization of current clinical imaging technologies and applications., (© 2022 American Association of Physicists in Medicine.)

Rationale and Objectives: The 3-fold purpose of this study was to (1) develop a method to relate measured differences in radiomics features in different computed tomography (CT) scans to one another and to true feature differences; (2) quantify minimum detectable change in radiomics features based on measured radiomics features from pairs of synthesized CT images acquired under variable CT scan settings, and (3) ascertain and inform the recommendations of the Quantitative Imaging Biomarkers Alliance (QIBA) for nodule volumetry., Materials and Methods: Images of anthropomorphic lung nodule models were simulated using resolution and noise properties for 297 unique imaging conditions. Nineteen morphology features were calculated from both the segmentation masks derived from the imaged nodules and from ground truth nodules. Analysis was performed to calculate minimum detectable difference of radiomics features as a function of imaging protocols in comparison to QIBA guidelines., Results: The minimum detectable differences ranged from 1% to 175% depending on the specific feature and set of imaging protocols. The results showed that QIBA protocol recommendations result in improved minimum detectable difference as compared to the range of possible protocols. The results showed that the minimum detectable differences may be improved from QIBA's current recommendation by further restricting the slice thickness requirement to be between 0.5 mm and 1 mm., Conclusion: Minimum detectable differences of radiomics features were quantified for lung nodules across a wide range of possible protocols. The results can be used prospectively to inform decision-making about imaging protocols to provide superior quantification of radiomics features., (Copyright © 2020 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.)

Purpose : Developing, validating, and evaluating a method for measuring noise texture directly from patient liver CT images (i.e., in vivo ). Approach : The method identifies target regions within patient scans that are least likely to have major contribution of patient anatomy, detrends them locally, and measures noise power spectrum (NPS) there using a previously phantom-validated technique targeting perceptual noise-non-anatomical fluctuations in the image that may interfere with the detection of focal lesions. Method development and validation used scanner-specific CT simulations of computational, anthropomorphic phantom (XCAT phantom, three phases of contrast-enhancement) with known ground truth of the NPS. Simulations were based on a clinical scanner (Definition Flash, Siemens) and clinically relevant settings (tube voltage of 120 kV at three dose levels). Images were reconstructed with filtered backprojection (kernel: B31, B41, and B50) and Sinogram Affirmed Iterative Reconstruction (kernel: I31, I41, and I50) using a manufacturer-specific reconstruction software (ReconCT, Siemens). All NPS measurements were made in the liver. Ground-truth NPS were taken as the sum of (1) a measurement in parenchymal regions of anatomy-subtracted (i.e., noise only) scans, and (2) a measurement in the same region of noise-free (pre-noise-insertion) images. To assess in vivo NPS performance, correlation of NPS average frequency ( f avg ), was reported. Sensitivity of accuracy [root-mean-square-error (RMSE)] to number of pixels included in measurement was conducted via bootstrapped pixel-dropout. Sensitivity of NPS to dose and reconstruction kernel was assessed to confirm that ground truth NPS similarities were maintained in patient-specific measurements. Results : Pearson and Spearman correlation coefficients 0.97 and 0.96 for f avg indicated good correlation. Results suggested accurate NPS measurements (within 5% total RMSE) could be acquired with ∼ 10 6    pixels . Conclusions : Relationships of similar NPS due to reconstruction kernel and dose were preserved between gold standard and observed in vivo estimations. The NPS estimation method was further deployed on clinical cases to demonstrate the feasibility of clinical analysis., (© 2021 Society of Photo-Optical Instrumentation Engineers (SPIE).)

Cells associated with an abnormal (cancerous) growth exchange flows, morph freely and grow hand-in-glove with their immediate environment, the extracellular matrix (ECM). The cell structure experiences two mass flows in counterflow. Flowing into the structure are nutrients and flowing out is refuse from the metabolically active biomass within. The physical effect of the evolution of the cell and extracellular structure is more flow and mixing in that space, that is, more mixing than in the absence of a biological growth in that space. The objective of the present theory is to predict the increase in the size of the cell cluster as a function of its structure, and also to predict the critical cluster sizes that mark the transitions from one distinct cluster configuration to the next. This amounts to predicting the timing and the main features of the transitions from single cell to clusters with two, four, eight and more cells, including larger clusters with cells organized on its outer surface. The predicted evolution of the size and configuration of the cell cluster is validated successfully by comparison with measurements from several independent studies of cancerous and non-cancerous growth patterns., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Purpose: Many interventional procedures aim at changing soft tissue perfusion or blood flow. One problem at present is that soft tissue perfusion and its changes cannot be assessed in an interventional suite because cone-beam computed tomography is too slow (it takes 4-10 s per volume scan). In order to address the problem, we propose a novel method called IPEN for Intra-operative four-dimensional soft tissue PErfusion using a standard x-ray system with No gantry rotation., Methods: IPEN uses two input datasets: (a) the contours and locations of three-dimensional regions-of-interest (ROIs) such as arteries and sub-sections of cancerous lesions, and (b) a series of x-ray projection data obtained from an intra-arterial contrast injection to contrast enhancement to wash-out. IPEN then estimates a time-enhancement curve (TEC) for each ROI directly from projections without reconstructing cross-sectional images by maximizing the agreement between synthesized and measured projections with a temporal roughness penalty. When path lengths through ROIs are known for each x-ray beam, the ROI-specific enhancement can be accurately estimated from projections. Computer simulations are performed to assess the performance of the IPEN algorithm. Intra-arterial contrast-enhanced liver scans over 25 s were simulated using XCAT phantom version 2.0 with heterogeneous tissue textures and cancerous lesions. The following four sub-studies were performed: (a) The accuracy of the estimated TECs with overlapped lesions was evaluated at various noise (dose) levels with either homogeneous or heterogeneous lesion enhancement patterns; (b) the accuracy of IPEN with inaccurate ROI contours was assessed; (c) we investigated how overlapping ROIs and noise in projections affected the accuracy of the IPEN algorithm; and (d) the accuracy of the perfusion indices was assessed., Results: The TECs estimated by IPEN were sufficiently accurate at a reference dose level with the root-mean-square deviation (RMSD) of 0.0027 ± 0.0001 cm -1 or 13 ± 1 Hounsfield unit (mean ± standard deviation) for the homogeneous lesion enhancement and 0.0032 ± 0.0005 cm -1 for the heterogeneous enhancement (N = 20 each). The accuracy was degraded with decreasing doses: The RMSD with homogeneous enhancement was 0.0220 ± 0.0003 cm -1 for 20% of the reference dose level. Performing 3 × 3 pixel averaging on projection data improved the RMSDs to 0.0051 ± 0.0002 cm -1 for 20% dose. When the ROI contours were inaccurate, smaller ROI contours resulted in positive biases in TECs, whereas larger ROI contours produced negative biases. The bias remained small, within ± 0.0070 cm -1 , when the Sorenson-Dice coefficients (SDCs) were larger than 0.81. The RMSD of the TEC estimation was strongly associated with the condition of the problem, which can be empirically quantified using the condition number of a matrix A z that maps a vector of ROI enhancement values z to projection data and a weighted variance of projection data: a linear correlation coefficient (R) was 0.794 (P < 0.001). The perfusion index values computed from the estimated TECs agreed well with the true values (R ≥ 0.985, P < 0.0001)., Conclusion: The IPEN algorithm can estimate ROI-specific TECs with high accuracy especially when 3 × 3 pixel averaging is applied, even when lesion enhancement is heterogeneous, or ROI contours are inaccurate but the SDC is at least 0.81., (© 2020 American Association of Physicists in Medicine.)

We propose to characterize the bias and variability of quantitative morphology features of lung lesions across a range of computed tomography (CT) imaging conditions. A total of 15 lung lesions were simulated (five in each of three spiculation classes: low, medium, and high). For each lesion, a series of simulated CT images representing different imaging conditions were synthesized by applying three-dimensional blur and adding correlated noise based on the measured noise and resolution properties of five commercial multislice CT systems, representing three dose levels ( CTDI vol of 1.90, 3.75, 7.50 mGy), three slice thicknesses (0.625, 1.25, 2.5 mm), and 33 clinical reconstruction kernels from five clinical scanners. The images were segmented using three segmentation algorithms and each algorithm was evaluated by computing a Sørensen-Dice coefficient between the ground truth and the segmentation. A series of 21 shape-based morphology features were extracted from both "ground truth" (i.e., preblur without noise) and "image rendered" lesions (i.e., postblur and with noise). For each morphology feature, the bias was quantified by comparing the percentage relative error in the morphology metric between the imaged lesions and the ground-truth lesions. The variability was characterized by calculating the average coefficient of variation averaged across repeats and imaging conditions. The active contour segmentation had the highest average Dice coefficient of 0.80 followed by 0.63 for threshold, and 0.39 for fuzzy c-means. The bias of the features was segmentation algorithm and feature-dependent, with sharper kernels being less biased and smoother kernels being more biased in general. The feature variability from simulated images ranged from 0.30% to 10% for repeats of the same condition and from 0.74% to 25.3% for different lesions in the same spiculation class. In conclusion, the bias of morphology features is dependent on the acquisition protocol in combination with the segmentation algorithm used and the variability is primarily dependent on the segmentation algorithm.

Thermal properties of compost bulking materials affect temperature and biodegradation during the composting process. Well determined thermal properties of compost feedstocks will therefore contribute to practical thermodynamic approaches. Thermal conductivity, thermal diffusivity, and volumetric heat capacity of 12 compost bulking materials were determined in this study. Thermal properties were determined at varying bulk densities (1, 1.3, 1.7, 2.5, and 5 times uncompacted bulk density), particle sizes (ground and bulk), and water contents (0, 20, 50, 80% of water holding capacity and saturated condition). For the water content at 80% of water holding capacity, saw dust, soil compost blend, beef manure, and turkey litter showed the highest thermal conductivity (K) and volumetric heat capacity (C) (K: 0.12-0.81 W/m degrees C and C: 1.36-4.08 MJ/m(3) degrees C). Silage showed medium values at the same water content (K: 0.09-0.47 W/m degrees C and C: 0.93-3.09 MJ/m(3) degrees C). Wheat straw, oat straw, soybean straw, cornstalks, alfalfa hay, and wood shavings produced the lowest K and C values (K: 0.03-0.30 W/m degrees C and C: 0.26-3.45 MJ/m(3) degrees C). Thermal conductivity and volumetric heat capacity showed a linear relationship with moisture content and bulk density, while thermal diffusivity showed a nonlinear relationship. Since the water, air, and solid materials have their own specific thermal property values, thermal properties of compost bulking materials vary with the rate of those three components by changing water content, bulk density, and particle size. The degree of saturation was used to represent the interaction between volumes of water, air, and solids under the various combinations of moisture content, bulk density, and particle size. The first order regression models developed in this paper represent the relationship between degree of saturation and volumetric heat capacity (r=0.95-0.99) and thermal conductivity (r=0.84-0.99) well. Improved knowledge of the thermal properties of compost bulking materials can contribute to improved thermodynamic modeling and heat management of composting processes.