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At least 397 records · Page 22

Automated Segmentation and Classification of Coral Using Fluid Lensing from Unmanned Airborne Platforms

In recent years, there has been a growing interest among biologists in monitoring the short and long term health of the worlds coral reefs. The environmental impact of climate change poses a growing threat to these biologically diverse and fragile ecosystems, prompting scientists to use remote sensing platforms and computer vision algorithms to analyze shallow marine systems. In this study, we present a novel method for performing coral segmentation and classification from aerial data collected from small unmanned aerial vehicles (sUAV). Our method uses Fluid Lensing algorithms to remove and exploit strong optical distortions created along the air-fluid boundary to produce cm-scale resolution imagery of the ocean floor at depths up to 5 meters. A 3D model of the reef is reconstructed using structure from motion (SFM) algorithms, and the associated depth information is combined with multidimensional maximum a posteriori (MAP) estimation to separate organic from inorganic material and classify coral morphologies in the Fluid-Lensed transects. In this study, MAP estimation is performed using a set of manually classified 100 x 100 pixel training images to determine the most probable coral classification within an interrogated region of interest. Aerial footage of a coral reef was captured off the coast of American Samoa and used to test our proposed method. 90 x 20 meter transects of the Samoan coastline undergo automated classification and are manually segmented by a marine biologist for comparison, leading to success rates as high as 85. This method has broad applications for coastal remote sensing, and will provide marine biologists access to large swaths of high resolution, segmented coral imagery.

algorithms segments classifications↗

Prong Segmentation using Point Set Transformers in Multiple View Neutrino Detectors

NOvA is a long-baseline neutrino experiment studying neutrino oscillations by detecting neutrinos from the NuMI beam at Fermilab. Its physics analysis relies on accurate prong segmentation, which involves matching each hit to its source particle and identifying the particle type. This task has commonly been addressed using a combination of traditional clustering algorithms and convolutional neural networks (CNNs). However, NOvA’s detector design presents data as two sparse and decoupled 2D images (XZ and YZ views) rather than a native 3D representation, posing a significant challenge for traditional CNN-based models. In this talk, we propose a novel neural network based on the Point Set Transformer. By treating detector hits as sparse point clouds and implementing a cross-view attention mechanism, our model enables efficient information mixing between both views. Evaluated on NOvA simulated data, our model achieves superior accuracy while requiring significantly fewer computational resources compared to other models. Furthermore, the model demonstrates great performance when applied to Liquid Argon Time Projection Chamber (LArTPC) data, which shows its potential as a universal prong segmentation algorithm for multiple view neutrino detectors.

Liu, Jiaxi [UC, Irvine]↗

WE-AB-BRA-05: Fully Automatic Segmentation of Male Pelvic Organs On CT Without Manual Intervention

Purpose: We aim to develop a fully automatic tool for accurate contouring of major male pelvic organs in CT images for radiotherapy without any manual initialization, yet still achieving superior performance than the existing tools. Methods: A learning-based 3D deformable shape model was developed for automatic contouring. Specifically, we utilized a recent machine learning method, random forest, to jointly learn both image regressor and classifier for each organ. In particular, the image regressor is trained to predict the 3D displacement from each vertex of the 3D shape model towards the organ boundary based on the local image appearance around the location of this vertex. The predicted 3D displacements are then used to drive the 3D shape model towards the target organ. Once the shape model is deformed close to the target organ, it is further refined by an organ likelihood map estimated by the learned classifier. As the organ likelihood map provides good guideline for the organ boundary, the precise contouring Result could be achieved, by deforming the 3D shape model locally to fit boundaries in the organ likelihood map. Results: We applied our method to 29 previously-treated prostate cancer patients, each with one planning CT scan. Compared with manually delineated pelvic organs, our method obtains overlap ratios of 85.2%±3.74% for the prostate, 94.9%±1.62% for the bladder, and 84.7%±1.97% for the rectum, respectively. Conclusion: This work demonstrated feasibility of a novel machine-learning based approach for accurate and automatic contouring of major male pelvic organs. It shows the potential to replace the time-consuming and inconsistent manual contouring in the clinic. Also, compared with the existing works, our method is more accurate and also efficient since it does not require any manual intervention, such as manual landmark placement. Moreover, our method obtained very similar contouring results as the clinical experts. Project is partially support by a grant from NCI 1R01CA140413.

60 APPLIED LIFE SCIENCES↗

In Situ Casting and Imaging of the Rat Airway Tree for Accurate 3D Reconstruction

The use of anatomically accurate, animal-specific airway geometries is important for understanding and modeling the physiology of the respiratory system. One approach for acquiring detailed airway architecture is to create a bronchial cast of the conducting airways. However, typical casting procedures either do not faithfully preserve the in vivo branching angles, or produce rigid casts that when removed for imaging are fragile and thus easily damaged. We address these problems by creating an in situ bronchial cast of the conducting airways in rats that can be subsequently imaged in situ using 3D micro-CT imaging. We also demonstrate that deformations in airway branch angles resulting from the casting procedure are small, and that these angle deformations can be reversed through an interactive adjustment of the segmented cast geometry. Animal work was approved by the Institutional Animal Care and Use Committee of Pacific Northwest National Laboratory.

Jacob, Rick E.↗

Covalent labeling of the Arabidopsis plasma membrane H + ‐ ATPase reveals 3D conformational changes involving the C‐terminal regulatory domain

The plasma membrane proton pump is the primary energy transducing, electrogenic ion pump of the plasma membrane in plants and fungi. Compared to its fungal counterpart, the plant plasma membrane proton pump's regulatory C‐terminal domain (CTD) contains an additional regulatory segment that links multiple sensory pathways regulating plant cell length through phosphorylation and recruitment of regulatory 14‐3‐3 proteins. However, a complete structural model of a plant proton pump is lacking. Here, we performed covalent labeling with mass spectrometric analysis (CL‐MS) on the Arabidopsis pump AHA2 to identify potential interactions between the CTD and the catalytic domains. Our results suggest that autoinhibition in the plant enzyme is much more structurally complex than in the fungal enzyme.

Blackburn, Matthew R. [Department of Biochemistry ↗

Generation of Fullspan Leading-Edge 3D Ice Shapes for Swept-Wing Aerodynamic Testing

The deleterious effect of ice accretion on aircraft is often assessed through dry-air flight and wind tunnel testing with artificial ice shapes. This paper describes a method to create fullspan swept-wing artificial ice shapes from partial span ice segments acquired in the NASA Glenn Icing Reserch Tunnel for aerodynamic wind-tunnel testing. Full-scale ice accretion segments were laser scanned from the Inboard, Midspan, and Outboard wing station models of the 65% scale Common Research Model (CRM65) aircraft configuration. These were interpolated and extrapolated using a weighted averaging method to generate fullspan ice shapes from the root to the tip of the CRM65 wing. The results showed that this interpolation method was able to preserve many of the highly three dimensional features typically found on swept-wing ice accretions. The interpolated fullspan ice shapes were then scaled to fit the leading edge of a 8.9% scale version of the CRM65 wing for aerodynamic wind-tunnel testing. Reduced fidelity versions of the fullspan ice shapes were also created where most of the local three-dimensional features were removed. The fullspan artificial ice shapes and the reduced fidelity versions were manufactured using stereolithography.

Icing↗

SU-E-J-262: Variability in Texture Analysis of Gynecological Tumors in the Context of An 18F-FDG PET Adaptive Protocol

Purpose: This study examines the effect on texture analysis due to variable reconstruction of PET images in the context of an adaptive FDG PET protocol for node positive gynecologic cancer patients. By measuring variability in texture features from baseline and intra-treatment PET-CT, we can isolate unreliable texture features due to large variation. Methods: A subset of seven patients with node positive gynecological cancers visible on PET was selected for this study. Prescribed dose varied between 45–50.4Gy, with a 55–70Gy boost to the PET positive nodes. A baseline and intratreatment (between 30–36Gy) PET-CT were obtained on a Siemens Biograph mCT. Each clinical PET image set was reconstructed 6 times using a TrueX+TOF algorithm with varying iterations and Gaussian filter. Baseline and intra-treatment primary GTVs were segmented using PET Edge (MIM Software Inc., Cleveland, OH), a semi-automatic gradient-based algorithm, on the clinical PET and transferred to the other reconstructed sets. Using an in-house MATLAB program, four 3D texture matrices describing relationships between voxel intensities in the GTV were generated: co-occurrence, run length, size zone, and neighborhood difference. From these, 39 textural features characterizing texture were calculated in addition to SUV histogram features. The percent variability among parameters was first calculated. Each reconstructed texture feature from baseline and intra-treatment per patient was normalized to the clinical baseline scan and compared using the Wilcoxon signed-rank test in order to isolate variations due to reconstruction parameters. Results: For the baseline scans, 13 texture features showed a mean range greater than 10%. For the intra scans, 28 texture features showed a mean range greater than 10%. Comparing baseline to intra scans, 25 texture features showed p <0.05. Conclusion: Variability due to different reconstruction parameters increased with treatment, however, the majority of texture features showed significant changes during treatment independent of reconstruction effects.

60 APPLIED LIFE SCIENCES↗

Morphing: A Novel Approach to Astronaut Suit Sizing

The fitting of a spacesuit to an astronaut is an iterative process consisting of two parts. The first uses anthropometric data to provide an approximation of the suit components that will fit the astronaut. The second part is the subjective fitting, where small adjustments are made based on the astronaut s preference. By providing a better approximation of the correct suit components, the entire fit process time can be reduced significantly. The goals of this project are twofold: (1) To evaluate the effectiveness of the existing sizing algorithm for the Mark III Hybrid suit and (2) to determine what additional components are needed in order to provide adequate sizing for the existing astronaut population. A single subject was scanned using a 3D whole-body scanner (VITUS 3D) in the Mark III suit in eight different poses and four subjects in minimal clothing were also scanned in similar poses. The 3D external body scans of the suit and the subject are overlaid and visually aligned in a customized MATLAB program. The suit components were contracted or expanded linearly along the subjects limbs to match the subjects segmental lengths. Two independent measures were obtained from the morphing program on four subjects and compared with the existing sizing information. Two of the four subjects were in correspondence with the sizing algorithm and morphing results. The morphing outcome for a third subject, incompatible with the suit, suggested that an additional arm element at least 6 inches smaller than the existing smallest suit component would need to be acquired. The morphing result of the fourth subject, deemed incompatible with the suit using the sizing algorithm, indicated a different suit configuration which would be compatible. This configuration matched with the existing suit fit check data.

Margerum, Sarah↗

Comparison of automated chemical-guided segmentation and human annotation of soil organic matter in X-ray microcomputed tomography imaging in contrasted soil types

Soil organic matter (OM) formation and persistence is strongly influenced by the spatial distribution of organic substrates and microscale soil heterogeneity by dictating OM accessibility to microorganisms. However, traditional size and/or density fractionation techniques disrupt aggregate architecture, eliminating spatial information needed to fully understand intra-aggregate OM distribution. To quantify three-dimensional OM spatial distribution and automate segmentation in X-ray microcomputed tomography (µCT) imaging without human annotation bias, we developed an iodine gas vapor (I2) based staining workflow that eliminates labor-intensive manual annotation while maintaining segmentation accuracy, using aggregates from four taxonomically diverse soils (Xerofluvent, Haploxeroll Sphagnofibrist, Palehumult) with an 8-fold range of soil organic carbon. Human annotation of 10 µCT slices by the experienced and inexperienced annotators resulted in variations up to 3% in the Dice similarity coefficient (DSC), reflecting a degree of inherent subjectivity of manual labeling. Such inconsistencies are expected to compound as the number of manually annotated slices increases. Dual-energy µCT imaging at 33.1 keV (below the iodine (I) K-edge) and 33.2 keV (above the I K-edge) was used to resolve aggregate microstructure following I2 staining. The automated image subtraction pipeline identified OM regions by the I Kedge induced brightness increases, achieving DSC values of 0.58–0.83 relative to an experienced annotator. Sensitivity analyses revealed that the reconstruction alpha value—optimized via the open-source tool TomocuPy—and the 3D registration slice count were the primary determinants of accuracy, providing a novel benchmark for dual-energy soil imaging. The pipeline without GPU acceleration achieved 9.6 to 43.2 times faster than manual annotation. Using GPU-accelerated image post-processing and affine transformation matrices, the pipeline successfully segmented OM elements for large-scale datasets (3232×3232 pixel, 2048 slices) within ~5200 s from raw file acquisition to segmented output. The high-throughput approach enables the quantification of OM spatial distribution across diverse and heterogeneous soil.

Soil microbial biomass↗

SU-F-303-17: Real Time Dose Calculation of MRI Guided Co-60 Radiotherapy Treatments On Free Breathing Patients, Using a Motion Model and Fast Monte Carlo Dose Calculation

Purpose: To demonstrate real-time dose calculation of free-breathing MRI guided Co−60 treatments, using a motion model and Monte-Carlo dose calculation to accurately account for the interplay between irregular breathing motion and an IMRT delivery. Methods: ViewRay Co-60 dose distributions were optimized on ITVs contoured from free-breathing CT images of lung cancer patients. Each treatment plan was separated into 0.25s segments, accounting for the MLC positions and beam angles at each time point. A voxel-specific motion model derived from multiple fast-helical free-breathing CTs and deformable registration was calculated for each patient. 3D images for every 0.25s of a simulated treatment were generated in real time, here using a bellows signal as a surrogate to accurately account for breathing irregularities. Monte-Carlo dose calculation was performed every 0.25s of the treatment, with the number of histories in each calculation scaled to give an overall 1% statistical uncertainty. Each dose calculation was deformed back to the reference image using the motion model and accumulated. The static and real-time dose calculations were compared. Results: Image generation was performed in real time at 4 frames per second (GPU). Monte-Carlo dose calculation was performed at approximately 1frame per second (CPU), giving a total calculation time of approximately 30 minutes per treatment. Results show both cold- and hot-spots in and around the ITV, and increased dose to contralateral lung as the tumor moves in and out of the beam during treatment. Conclusion: An accurate motion model combined with a fast Monte-Carlo dose calculation allows almost real-time dose calculation of a free-breathing treatment. When combined with sagittal 2D-cine-mode MRI during treatment to update the motion model in real time, this will allow the true delivered dose of a treatment to be calculated, providing a useful tool for adaptive planning and assessing the effectiveness of gated treatments.

60 APPLIED LIFE SCIENCES↗

Structural elements and collapse regimes in 3D flows on a slope

The mechanisms and structural elements of an instability whose development results in the collapse of flow fragments have been studied in the scope of the Hamilton version of the 'shallow water' 3D model on a slope. The study indicated that the 3D model differs from its 2D analog in a more varied set of collapsing solutions. In particular, the solutions describing anisotropic collapse, during which the area of a collapsing fragment in contact with the slope contracts into a segment rather than a point, exist together with the solutions describing radially symmetric (isotropic) collapse.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

3D-Stereoscopic Analysis of Solar Active Region Loops: I: SoHo/EIT Observations at Temperatures of 1.0-1.5 MK

The three-dimensional (3D) structure of solar active region NOAA 7986 observed on 1996 August 30 with the Extrem-ultraviolet Imaging Telescope (EIT) onboard the Solar and Heliospheric Observatory (SoHO) is analyzed. We develop a new method of Dynamic Stereoscopy to reconstruct the 3D geometry of dynamically changing loops, which allows us to determine the orientation of the loop plane with respect to the line-of-sight, a prerequisite to correct properly for projection effects in 3D loop models. With this method and the filter-ratio technique applied to EIT 171 A and 195 A images we determine the 3D coordinates (x(s), y(s), z(s)), the loop width) w(s), the electron density n(sub e)(s), and the electron temperature T(sub e)(s) as function of the loop length s for 30 loop segments. Fitting the loop densities with an exponential density model n(sub e)(h) we find that the so inferred scale height temperatures, T(sub e)(sup lambda) = 1.22 +/- 0.23 MK, match closely the EIT filter-ratio temperatures, T(sub e)(sup FIT) = 1.21 +/- 0.06 MK. We conclude that these rather large-scale loops (with heights of h approx. equals 50 - 200 Mm) that dominate EIT 171 A images are close to thermal equilibrium. Most of the loops show no significant thickness variation w(s), but many exhibit a trend of increasing temperature (dT/ds greater than 0) above the footpoint.

Aschwanden, Markus J.↗

SU-E-T-611: Photon and Neutron Peripheral Dose Ratio for Low (6 MV) and High (15 MV) Energy for Treatment Selection

Purpose: Differences between radiotherapy techniques and energies, can offer improvements in tumor coverage and organs at risk preservation. However, a more complete decision should include peripheral doses delivered to the patient. The purpose of this work is the balance of photon and neutron peripheral doses for a prostate case solved with 6 different treatment modalities. Methods: Inverse and Forward IMRT and 3D-CRT in 6 and 15 MV for a Siemens Primus linac, using the same CT data set and contours. The methodology described in [1], was used with the TNRD thermal neutron detector [2] for neutron peripheral dose estimation at 7 relevant organs (colon, esophagus, stomach, liver, lung, thyroid and skin). Photon doses were estimated for these organs by terms of the algorithm proposed in [3]. Plans were optimized with the same restrictions and limited to 30 segments in the Inverse case. Results: A similar photon peripheral dose was found comparing 6 and 15 MV cases with slightly higher values of (1.9 ± 1.6) % in mean, for the 6 MV cases. Neutron presence when using 15 MV, represents an increase in peripheral dose of (18 ± 17) % in average. Due to the higher number of MU used in Inverse IMRT, an increasing of (22 ± 3) % in neutron dose is found related to Forward and 3D-CRT plans. This corresponds to photon doses within 44 and 255 mSv along the organs, for a dose prescription of 68 Gy at the isocenter. Conclusion: Neutron and photon peripheral doses for a prostate treatment planified in 6 different techniques have been analyzed. 6 MV plans are slightly more demanding in terms of photon peripheral doses. Inverse technique in 15 MV has Result to be the most demanding one in terms of total peripheral doses, including neutrons and photons.

61 RADIATION PROTECTION AND DOSIMETRY↗

3D Imaging of Microbial Biofilms: Integration of Synchrotron Imaging and an Interactive Visualization Interface

Understanding the interactions of structured communities known as “biofilms” and other complex matrixes is possible through the X-ray micro tomography imaging of the biofilms. Feature detection and image processing for this type of data focuses on efficiently identifying and segmenting biofilms and bacteria in the datasets. The datasets are very large and often require manual interventions due to low contrast between objects and high noise levels. Thus new software is required for the effectual interpretation and analysis of the data. This work specifies the evolution and application of the ability to analyze and visualize high resolution X-ray micro tomography datasets.

Biofilm Viewer↗

Mechanism of formation of wiggly compaction bands in porous sandstone: 2. Numerical simulation using discrete element method

Wiggly compaction bands in porous aeolian s andstone vary from chevron shape to wavy shape to nearly straight. In some outcrops these variations occur along a single band. Here, a bonded close-packed discrete element model is used to investigate what mechanical properties control the formation of wiggly compaction bands (CBs). To simulate the volumetric yielding failure of porous sandstone, a discrete element shrinks when the force state of one of its bonds reaches the yielding cap defined by the failure force and the aspect ratio (k) of the yielding ellipse. A Matlab code “MatDEM 3D ” has been developed on the basis of this enhanced discrete element method. Mechanical parameters of elements are chosen according to the elastic properties and the strengths of porous sandstone. In numerical simulations, the failure angle between the band segment and maximum principle stress decreases from 90° to approximately 45° as k increases from 0.5 to 2, and compaction bands vary from straight to chevron shape. With increasing strain, subsequent compaction occurs inside or beside compacted elements, which leads to further compaction and thickening of bands. The simulations indicate that a greater yielding stress promotes chevron CBs, and a greater cement strength promotes straight CBs. Combined with the microscopic analysis introduced in the companion paper, we conclude that the shape of wiggly CBs is controlled by the mechanical properties of sandstone, including the aspect ratio of the yielding ellipse, the cri tical yielding stress, and the cement strength, w hich are d etermined primarily by petrophysical attributes, e.g., grain sorting, porosity, and cementation.

58 GEOSCIENCES↗

Van der Waals Nanowires with Continuously Variable Interlayer Twist and Twist Homojunctions

Abstract Moiré patterns at van der Waals interfaces between twisted 2D crystals give rise to distinct optoelectronic excitations, as well as, narrowly dispersive bands responsible for correlated electron phenomena. Contrasting with the conventional, mechanically stacked planar twist moirés, recent work shows twisted van der Waals interfaces spontaneously formed in nanowires of layered crystals, where Eshelby twist due to axial screw dislocations stabilizes a chiral structure with small interlayer rotation. Here, the realization of tunable twist in germanium(II) sulfide (GeS) van der Waals nanowires is reported. Tapered nanowires host continuously variable interlayer twist. Homojunctions between dislocated (chiral) and defect‐free (achiral) segments are obtained by triggering the emission of axial dislocations during growth. Measurements across such junctions, implemented here using local absorption and luminescence spectroscopy, provide a convenient tool for detecting twist effects. The results identify a versatile system for 3D twistronics, probing moiré physics, and for realizing moiré architectures without equivalent in planar systems.

Sutter, Peter↗

Rough-Wall Turbulent Heat Transfer Experiments in Hypersonic Free Flight

Experiments are being conducted in the NASA Ames Hypervelocity Free Flight Aerodynamic Facility to quantify the effects on turbulent convective heat transfer of surface roughness representative of a new class of 3D woven thermal protection system mRough-wall turbulent heat transfer measurements were obtained on ballistic-range models in hypersonic flight in the NASA Ames Hypervelocity Free Flight Aerodynamic Facility. Each model had three different surface textures on segments of the conic frustum: smooth wall, sand roughness, and a pattern roughness, thus providing smooth-wall and sand-roughness reference data for each test. The pattern roughness was representative of a woven thermal protection system material developed by NASA's Heatshield for Extreme Entry Environment Technology project. The tests were conducted at launch speeds of 3.2 km/s in air at 0.15 atm. Roughness Reynolds numbers, k+, ranged for 12 to 70 for the sand roughness, and as high as 200 for the pattern roughness. Boundary-layer parameters required for calculating k+ were evaluated using computational fluid dynamics simulations. The effects of pattern roughness are generally characterized by an equivalent sand roughness determined with a correlation developed from experimental data obtained on specifically-designed roughness patterns that do not necessarily resemble real TPS materials. Two sand roughness correlations were examined: Dirling and van Rij, et al. Both gave good agreement with the measured heat-flux augmentation for the two larger pattern roughness heights tested, but not for the smallest height tested. It has yet to be determined whether this difference is due to limitations in the experimental approach, or due to limits in the correlations used. Future experiments are planned that will include roughness patterns more like those used in developing the equivalent sand roughness correlations.aterials being developed by NASA's Heatshield for Extreme Entry Environment Technology (HEEET) project. Data were simultaneously obtained on sand-grain roughened surfaces and smooth surfaces, which can be compared with previously obtained data. Results are presented in this extended abstract for one roughness pattern. The full paper will include results from three roughness patterns representing virgin HEEET, nominal turbulent ablated HEEET, and twice the roughness of nominal turbulent ablated HEEET. Results will be used to compare with commonly used equivalent sand grain roughness correlations.

pattern roughness↗

Accelerated vortex dynamics across the magnetic 3D-to-2D crossover in disordered superconductors

Disorder can have remarkably disparate consequences in superconductors, driving superconductor–insulator transitions in ultrathin films by localizing electron pairs and boosting the supercurrent carrying capacity of thick films by localizing vortices (magnetic flux lines). Though the electronic 3D-to-2D crossover at material thicknesses d ~ ξ (coherence length) is well studied, a similarly consequential magnetic crossover at d ~ L c (pinning length) that should drastically alter material properties remains largely underexamined. According to collective pinning theory, vortex segments of length L c bend to adjust to energy wells provided by point defects. Consequently, if d truncates L c , a change from elastic to rigid vortex dynamics should increase the rate of thermally activated vortex motion S. Here, we characterize the dependence of S on sample thickness in Nb and cuprate films. The results for Nb are consistent with collective pinning theory, whereas creep in the cuprate is strongly influenced by sparse large precipitates. In conclusion, we leverage the sensitivity of S to d to determine the generally unknown scale L c , establishing a new route for extracting pinning lengths in heterogeneously disordered materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗