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MTIP Single Particle Imaging (Spinifel) v0.1.0
Performs Multi-Tiered Iterative Phasing for Single Particle Imaging. The Spinifel code uses distributed computing (using MPI and Legion) to spread work across many compute nodes. On-node computation is accelerated using GPGPUs (using CuPy, and CUDA).
Reference data, predictors, and probability grids for forest degradation classes in three sites in the Brazilian Amazon
Forest degradation by fires and selective logging is widespread in the Amazon region. We implemented a gradient boosted classification modeling framework to classify intact, logged, and burned forests at three Amazonian sites: Feliz Natal Municipality and Xingu Indigenous Territory in Mato Grosso State, and Saracá-Taquera National Forest in Pará State. We used forest degradation history from Landsat time-series as reference data and textural metrics derived from PlanetScope images as predictors. Textural metrics were computed using the Gray-Level Co-Occurrence Matrix (GLCM) textural technique. Included in the attached zip file are ten files: - a shapefile containing the reference data (fire and selective logging polygons and year of event) for each site; - a multiband tif file containing the 8 GLCM metrics used as predictors (Mean, Variance, Homogeneity, Contrast, Dissimilarity, Entropy, Angular Second Moment, Correlation) at the original PlanetScope resolution (3.125m) for each site; - a multiband tif file containing the 72 aggregated GLCM metrics used as predictors (Mean, Variance, Homogeneity, Contrast, Dissimilarity, Entropy, Angular Second Moment, and Correlation aggregated using the mean, first quartile, third quartile, maximum, median, minimum, root mean square, standard deviation, and skewness statistics) at 562m resolution for each site; - a multiband tif file containing the 3 probability grids for either intact, logged, or burned forests at the aggregation resolution (562m) for each site.
Understanding and Overcoming Water-induced Interfacial Degradation in Si Modules (Final Technical Report)
Moisture ingress is an established issue for photovoltaic module durability. Durability studies probing moisture effects typically evaluate performance losses at the module level, attributing global power losses to the overall humidity condition of the test environment while leaving local module behavior unknown. This project successfully develops an in situ short-wave infrared probe of moisture content in PV modules with demonstrated detection limits better than 100 ppm in EVA-encapsulated Al-BSF and PERC architectures (66 µg/cm3) and applicability across the range of terrestrial conditions. Combining this optical moisture quantification method (water reflectometry detection, WaRD) with peel testing of interfaces, biased photoluminescence imaging of performance, and first principles computation, we correlate module moisture content and cell performance over the course of accelerated damp heat tests. By performing multi-level humidity and thermal accelerated testing over thousands of hours (0, 65 and 85% RH and 25, 65, and 85°C), we are able to attribute effects of individual environmental stresses and the dependence on module architecture. Using first-principles computational chemistry, we find that the decomposition of EVA to acetic acid (Norrish II) is thermodynamically preferred over a pathway to acetaldehyde (Norrish I), elucidating the underlying chemistry of encapsulant degradation. We also find it is likely that water segregates to the stable interfaces of the cell, especially the SiNx/EVA interface. We find that moisture is strongly correlated with reduction in adhesion at the interfaces of the cells, particularly at Ag fingers. We show uniquely that the peel strength required to delaminate the encapsulant from the front of the cell depends not only on the exposure to a high heat and humid environment, but also to the moisture content during the mechanical testing, indicating an important interaction between when mechanical stresses are faced in terms of the moisture content of the module and its durability. We find that the background sheet resistance (that is, the sheet resistance rise not attributable to finger interruptions or cracks) is substantially higher in the backsheet mini-modules vs glass-glass packages when humidity and temperature are faced. This increase in power loss due to the background resistance increase over time in damp heat in glass-backsheet modules resulted in ~3-4% larger decrease in relative PCE compared to glass-glass modules. In glass-backsheet modules, the effect of the moisture dose alone is comparable or greater than that of the combined temperature and water term, suggesting that glass-backsheet modules are overall more susceptible to moisture induced performance loss. Finally, we show that thin film PV modules are amenable to WaRD measurement, based on the ability to detect moisture in POE encapsulants or in the cell stack itself. The ease of WaRD measurement and its few requirements on the bill of materials should enable broad applicability of this technique for studying the effects of moisture in PV.
Z Line VISAR Analysis with the LineVISAR SMASH Class
The Z line VISAR system (ZLV) is a spatially-resolved velocimeter that measures surface velocities in high-energy density experiments on the Z Pulsed Power Facility to facilitate the investigation of fusion, power flow, and dynamic material physics. The data measured in these experiments are analyzed with the LineVISAR SMASH class, a MATLAB software suite that provides tools for data importation, streak image correction, spatiotemporal registration, wrapped phase computation, phase unwrapping, shock handling, and velocity calculation. This report overviews the LineVISAR class, discusses its use, provides example implementations, and supplies analysis specifics not typically recorded in journal publications.
Dynamic three-dimensional maps of solute concentration and solute arrival times in synthetic and geologic porous media
Experimental and training data associated with the publication entitled ‘Three-Dimensional Permeability Inversion Using Convolutional Neural Networks and Positron Emission Tomography’ (published in WRR, DOI: 10.1029/2021WR031554). The dataset contain three-dimensional maps of various properties on four geologic rock cores obtained from X-ray Computed Tomography and Positron Emission Tomography imaging measurements. The synthetic training dataset used in the publication is also attached.
Diagnosing Malaria Patients with Plasmodium falciparum and vivax Using Deep Learning for Thick Smear Images
We propose a new framework, PlasmodiumVF-Net, to analyze thick smear microscopy images for a malaria diagnosis on both image and patient-level. Our framework detects whether a patient is infected, and in case of a malarial infection, reports whether the patient is infected by Plasmodium falciparum or Plasmodium vivax. PlasmodiumVF-Net first detects candidates for Plasmodium parasites using a Mask Regional-Convolutional Neural Network (Mask R-CNN), filters out false positives using a ResNet50 classifier, and then follows a new approach to recognize parasite species based on a score obtained from the number of detected patches and their aggregated probabilities for all of the patient images. Reporting a patient-level decision is highly challenging, and therefore reported less often in the literature, due to the small size of detected parasites, the similarity to staining artifacts, the similarity of species in different development stages, and illumination or color variations on patient-level. We use a manually annotated dataset consisting of 350 patients, with about 6000 images, which we make publicly available together with this manuscript. Our framework achieves an overall accuracy above 90% on image and patient-level.
In Search of Optimum Fresh-Cut Raw Material: Using Computer Vision Systems as a Sensory Screening Tool for Browning-Resistant Romaine Lettuce Accessions
The popularity of ready-to-eat (RTE) salads has prompted novel technology to prolong the shelf life of their ingredients. Fresh-cut romaine lettuce is widely used in RTE salads; however, its tendency to quickly discolor continues to be a challenge for the industry. Selecting the ideal lettuce accessions for use in RTE salads is essential to ensure maximum shelf life, and it is critical to have a practical way to assess and compare the quality of multiple lettuce accessions that are being considered for use in fresh-cut applications. Thus, in this work we aimed to determine whether a computer vision system (CVS) composed of image acquisition, processing, and analysis could be effective to detect visual quality differences among 16 accessions of fresh-cut romaine lettuce during postharvest storage. The CVS involved a post-capturing color correction, effective image segmentation, and calculation of a browning index, which was tested as a predictor of quality and shelf life of fresh-cut romaine lettuce. The results demonstrated that machine vision software can be implemented to replace or supplement the scoring of a trained panel and instrumental quality measurements. Overall visual quality, a key sensory parameter that determines food preferences and consumer behavior, was highly correlated with the browning index, with a Pearson correlation coefficient of −0.85. Other important sensory decision parameters were also strongly or moderately correlated with the browning index, with Pearson correlation coefficients of −0.84 for freshness, 0.79 for off odor, and 0.57 for browning. The ranking of the accessions according to quality acceptability from the sensory evaluation produced a similar pattern to those obtained with the CVS. This study revealed that multiple lettuce accessions can be effectively benchmarked for their performance as fresh-cut sources via a CVS-based method. Future opportunities and challenges in using machine vision image processing to predict consumer preferences for RTE salad greens is also discussed.
Dynamically Reconfigurable Data Readout of Pixel Detectors for Automatic Synchronization with Data Acquisition Systems
Reconfigurable detectors with dynamically selectable sensing and readout modes are highly desirable for implementing edge computing as well as enabling advanced imaging techniques such as foveation. The concept of a camera system capable of simultaneous passive imaging and dynamic ranging in different regions of the detector is presented. Such an adaptive-autonomous detector with both spatial and temporal control requires programmable window of exposure (time frames), ability to switch between readout modes such as full-frame imaging and zero-suppressed data, modification of the number of pixel data bits and independent programmability for distinct detector regions. In this work, a method is presented for seamlessly changing time frames and readout modes without data corruption while still ensuring that the data acquisition system (DAQ) does not need to stop and resynchronize at each change of setting, thus avoiding significant dead time. Data throughput is maximized by using a minimum unique data format, rather than lengthy frame headers, to differentiate between consecutive frames. A data control and transmitter (DCT) synchronizes data transfer from the pixel to the periphery, reconfigures the data to transmit it serially off-chip, while providing optimized decision support based on a DAQ definable mode. Measurements on a test structure demonstrate that the DCT can operate at 1 GHz in a 65 nm LP CMOS process.
Shape Analytics for In Situ Fine Root Measurements
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Characterization of damage processes in Montney siltstone under triaxial compression using acoustic emission and diagnostic imaging
SUMMARY Crack nucleation and rock failure processes in a fine-grained siltstone (Montney Formation) under triaxial compression are investigated using combined diagnostic techniques, including ultrasonic-wave measurement, acoustic-emission (AE) monitoring, computed tomography (CT) scanning, and thin-section imaging. The sample displays a weak-to-moderate inherent seismic anisotropy and noticeable stress-induced anisotropy prior to failure. No AE event was detected until the applied axial stress reached 95 per cent of the peak value. The signal-to-noise ratio is relatively low, however, and detectable AE events are more diffuse than those observed in highly brittle rocks. The AE locations correlate with a shear fracture zone imaged by CT scanning. AE moment-tensor analysis reveals that events with larger relative magnitudes are characterized by high volumetric (tensile or compressive) components, and the initiation of the failure zone is dominated by combined shear-tensile (ST) failure. Stress inversion of the AE events with high tensile components is in good agreement with the known applied stress. Microscopic imaging of thin sections from the failed sample shows that the failure zone is an en echelon structure consisting of a major fracture with branching micro and minor cracks. This failure mechanism is consistent with a ST source mechanism and is interpreted to be associated with the fine granular structure and mineral composition of Montney siltstone.
In situ tumor model for longitudinal in silico imaging trials
Abstract Objective.In this article, we introduce a computational model for simulating the growth of breast cancer lesions accounting for the stiffness of surrounding anatomical structures.Approach.In our model, ligaments are classified as the most rigid structures while the softer parts of the breast are occupied by fat and glandular tissues As a result of these variations in tissue elasticity, the rapidly proliferating tumor cells are met with differential resistance. It is found that these cells are likely to circumvent stiffer terrains such as ligaments, instead electing to proliferate preferentially within the more yielding confines of the breast’s soft topography. By manipulating the interstitial tumor pressure in direct proportion to the elastic constants of the tissues surrounding the tumor, this model thus creates the potential for realizing a database of unique lesion morphology sculpted by the distinctive topography of each local anatomical infrastructure. We modeled the growth of simulated lesions within volumes extracted from fatty breast models, developed by Graffet alwith a resolution of 50μm generated with the open-source and readily available Virtual Imaging Clinical Trials for Regulatory Evaluation (VICTRE) imaging pipeline. To visualize and validate the realism of the lesion models, we leveraged the imaging component of the VICTRE pipeline, which replicates the siemens mammomat inspiration mammography system in a digital format. This system was instrumental in generating digital mammogram (DM) images for each breast model containing the simulated lesions.Results.By utilizing the DM images, we were able to effectively illustrate the imaging characteristics of the lesions as they integrated with the anatomical backgrounds. Our research also involved a reader study that compared 25 simulated DM regions of interest (ROIs) with inserted lesions from our models with DM ROIs from the DDSM dataset containing real manifestations of breast cancer. In general the simulation time for the lesions was approximately 2.5 hours, but it varied depending on the lesion’s local environment.Significance.The lesion growth model will facilitate and enhance longitudinal in silico trials investigating the progression of breast cancer.
Advancing the Frontiers of Deep Learning for Low-Dose 3D Cone-Beam CT Reconstruction
X-ray computed tomography (CT) is an important noninvasive medical imaging modality for studying the structural details of internal organs. Image reconstruction in CT is an inverse problem of recovering an object's internal structure from the absorption profile of X-ray beams (sinogram) measured using a detector. The classical variational approach for CT reconstruction minimizes an energy functional using an appropriate iterative algorithm. Motivated by the success of deep learning (DL), researchers have begun to leverage training data and enhanced computing capabilities in recent years to produce high-fidelity reconstructed images. Nonetheless, much of the academic research in DL algorithms for CT has focused primarily on the two-dimensional setting (with simplified forward operators and noise model) for proofs-of-concept, and a comprehensive benchmarking of various classical and data-driven CT reconstruction approaches has not beenundertaken. The key objective of our CT reconstruction grand challenge was to promote methodological advancements for both classical and DL-based approaches for clinical CT with a reasonably accurately simulated 3D CT forward operator and noise model. We have utilized the publicly available LIDC-IDRI dataset and simulated sinograms and FDK images corresponding to two dose levels (clinical- and low-dose, constituting two tracks of the challenge) starting from the normal-dose images as the ground truth. In this paper, we summarize the motivation, context, and results of our challenge, and highlight the future research directions in DL for clinical CT.
Computational design of passivants for CdTe grain boundaries
CdTe is the second most-widely deployed photovoltaic (PV) material due to its high efficiency and low manufacturing costs. Currently, polycrystalline CdTe (poly-CdTe) has a record efficiency of similar to 22%, which is still well below the theoretical limit (similar to 30%). Polycrystalline CdTe films that have incorporated Cl or Se show higher efficiency, possibly due to the segregation of these ions to the grain boundaries (GBs), where they may passivate the dangling bonds. However, the efficiency enhancement mechanisms of passivants in CdTe GBs, and the feasibility of employing alternative passivants, have not been well explored. Here, we present a systematic computational study of CdTe GBs with potential passivants, namely S, P, As, Se, and Sb on Te sites, and Na, Mg, Al, Sc, Cu, and Zn on Cd sites. Density functional theory (DFT) calculations were performed on GB dislocation core structures derived from scanning transmission electron microscopy (STEM) images of a model GB (bicrystal). We computed the segregation thermodynamics, electronic density of states, and charge variations near doped CdTe GBs. We find that segregation of impurities to GBs is thermodynamically favorable. For a Te-terminated core, Se, S, and P on Te sites effectively reduce midgap states. For both Cd-and Te-terminated dislocation cores, Sc and Al reduce midgap states when substituted for Cd atoms. Overall, the greatest improvement was achieved with co-doping, i.e. simultaneously substituting Te with Se and substituting Cd with Cu or Al. The elimination of midgap states is predicted to increase the photovoltaic efficiency of CdTe by reducing the recombination at grain boundaries.
Evaluating generative networks using Gaussian mixtures of image features
We develop a measure for evaluating the performance of generative networks given two sets of images. A popular performance measure currently used to do this is the Fréchet Inception Distance (FID). However, FID assumes that images featurized using the penultimate layer of Inception follow a Gaussian distribution. This assumption allows FID to be easily computed, since FID uses the 2-Wasserstein distance of two Gaussian distributions fitted to the featurized images. However, we show that Inception features of the ImageNet dataset are not Gaussian; in particular, each marginal is not Gaussian. To remedy this problem, we model the featurized images using Gaussian mixture models (GMMs) and compute the 2-Wasserstein distance restricted to GMMs. We define a performance measure, which we call WaM, on two sets of images by using inception (or another classifier) to featurize the images, estimate two GMMs, and use the restricted 2-Wasserstein distance to compare the GMMs. We experimentally show the advantages of WaM over FID, including how FID is more sensitive than WaM to image perturbations. By modelling the non-Gaussian features obtained from inception as GMMs and using a GMM metric, we can more accurately evaluate generative network performance.
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties
Abstract Motivation BISCAP is a state-of-the-art tool for automatically characterizing biofilm images obtained from Optical Coherence Tomography. Limited availability of other software tools is reported in the field. BISCAP’s first version processes 2D images only. Processing 3D images is a problem of greater scientific relevance since it deals with the entire structure of biofilms instead of their 2D slices. Results Building on the image-processing principles and algorithms proposed earlier for 2D images, these were adapted to the 3D case, and a more general implementation of BISCAP was developed. The primary goal concerns the extension of the initial methodology to incorporate the depth axis in 3D images; multiple improvements were also made to boost computational performance. The calculation of structural properties and visual outputs was extended to offer new insights into the 3D structure of biofilms. BISCAP was tested using 3D images of biofilms with different morphologies, consistently delivering accurate characterizations of 3D structures in a few minutes using standard laptop machines. Low user dependency is required for image analysis. Availability and implementation BISCAP is available from https://github.com/diogonarciso/BISCAP. All images used in the tutorials and the validation examples are available from https://web.fe.up.pt/∼fgm/biscap3d.
Recurrent Activity from Active Asteroid (248370) 2005 QN 173 : A Main-belt Comet
We present archival observations of main-belt asteroid (248370) 2005 QN 173 (also designated 433P) that demonstrate this recently discovered active asteroid (a body with a dynamically asteroidal orbit displaying a tail or coma) has had at least one additional apparition of activity near perihelion during a prior orbit. We discovered evidence of this second activity epoch in an image captured 2016 July 22 with the DECam on the 4 m Blanco telescope at the Cerro Tololo Inter-American Observatory in Chile. As of this writing, (248370) 2005 QN 173 is just the eighth active asteroid demonstrated to undergo recurrent activity near perihelion. Our analyses demonstrate (248370) 2005 QN 173 is likely a member of the active asteroid subset known as main-belt comets, a group of objects that orbit in the main asteroid belt that exhibit activity that is specifically driven by sublimation. We implement an activity detection technique, wedge photometry, that has the potential to detect tails in images of solar system objects and quantify their agreement with computed antisolar and antimotion vectors normally associated with observed tail directions. We present a catalog and an image gallery of archival observations. The object will soon become unobservable as it passes behind the Sun as seen from Earth, and when it again becomes visible (late 2022) it will be farther than 3 au from the Sun. Our findings suggest (248370) 2005 QN 173 is most active interior to 2.7 au (0.3 au from perihelion), so we encourage the community to observe and study this special object before 2021 December.
Quantitative Comparisons of Image Quality for Flash X-Ray Detectors
Due to X-rays’ ability to penetrate materials, flash X-ray radiography can be used for high-speed measurements where direct optical access is not possible. Choice of detector has a pronounced impact on resulting image quality. Four different detector systems were evaluated with a 450kVp flash source to quantitatively compare image quality metrics. The scintillating digital detector had less image noise than the three different storage phosphor computed radiography detectors across all transmission levels, but lacked the spatial resolution of the computed radiography detectors. For the screens tested here, the HPX-DR digital system had the highest signal to noise ratio of 68.24 and contrast to noise ratio of 35.53, but had the lowest spatial resolution, resolving 2.5 line pairs per millimeter at 1.78% contrast. At a value of 37.59, the Flex GP imaging plate had a signal to noise value above its storage phosphor counterparts under a 450kVp flash source. For radiographic setups typically used for dynamic experiments, the Flex XL Blue and Flex HR detectors had signal to noise ratios of 18.44 and 26.56 respectively. The highest resolved spatial frequencies of the Flex GP, Flex XL Blue, and Flex HR with the flash source are 3.85, 5.00, and 3.85 line pairs per millimeter, respectively. In conclusion, the Flex GP detector had the best combination of signal to noise ratio, contrast to noise ratio, and spatial resolution under a flash source.