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At least 1,117 records · Page 62

Camera settings and biome influence the accuracy of citizen science approaches to camera trap image classification

Scientists are increasingly using volunteer efforts of citizen scientists to classify images captured by motion-activated trail cameras. The rising popularity of citizen science reflects its potential to engage the public in conservation science and accelerate processing of the large volume of images generated by trail cameras. While image classification accuracy by citizen scientists can vary across species, the influence of other factors on accuracy is poorly understood. Inaccuracy diminishes the value of citizen science derived data and prompts the need for specific best-practice protocols to decrease error. We compare the accuracy between three programs that use crowdsourced citizen scientists to process images online: Snapshot Serengeti, Wildwatch Kenya, and AmazonCam Tambopata. We hypothesized that habitat type and camera settings would influence accuracy. To evaluate these factors, each photograph was circulated to multiple volunteers. All volunteer classifications were aggregated to a single best answer for each photograph using a plurality algorithm. Subsequently, a subset of these images underwent expert review and were compared to the citizen scientist results. Classification errors were categorized by the nature of the error (e.g., false species or false empty), and reason for the false classification (e.g., misidentification). Our results show that Snapshot Serengeti had the highest accuracy (97.9%), followed by AmazonCam Tambopata (93.5%), then Wildwatch Kenya (83.4%). Error type was influenced by habitat, with false empty images more prevalent in open-grassy habitat (27%) compared to woodlands (10%). For medium to large animal surveys across all habitat types, our results suggest that to significantly improve accuracy in crowdsourced projects, researchers should use a trail camera set up protocol with a burst of three consecutive photographs, a short field of view, and determine camera sensitivity settings based on in situ testing. Accuracy level comparisons such as this study can improve reliability of future citizen science projects, and subsequently encourage the increased use of such data.

54 ENVIRONMENTAL SCIENCES↗

A Machine Learning Approach to Quantitative Analysis of Enamel Microstructure from Scanning Electron Microscopy Images

Dental enamel, the outermost tissue of mammalian teeth, must withstand a lifetime of wear and cyclic contact. To meet this demand, enamel possesses a combination of high hardness and resistance to fracture, properties that are typically mutually exclusive. The impressive damage tolerance has been attributed largely to decussation of the enamel rods, the principal unit of its microstructure. As such, enamel is inspiring the design of next‐generation structural materials. However, quantitative descriptions of the decussated enamel rod microstructure remain limited due to challenges encountered in applying computed tomography and in acquiring quality images appropriate for traditional digital processing methods. Here, a machine learning segmentation method is applied to images of the enamel obtained using scanning electron microscopy to support quantitative analysis of the microstructure. A pretrained convolutional neural network is used to expand the input training image dataset to allow the training of a random forest classifier, which ultimately segments the image with a very small training set ( n = 3 images). A validation of this segmentation method is presented, in addition to its application to calculate relevant microstructural parameters for images of tooth enamel from selected mammalian species. The methodology applied here is equally applicable to other hard tissues.

36 MATERIALS SCIENCE↗

Diagnostic imaging of hepatocellular carcinoma at community hospitals and their tertiary referral center in the era of LI-RADS: a quality assessment study

Purpose: To assess guideline compliance and quality of hepatocellular carcinoma, (HCC) diagnostic imaging within community hospitals (CH) and their Tertiary referral center (TRC) in a moderately high incidence region. Methods: Initial diagnostic workup CT/MRI scans of 251 patients (122 CH, 112 TRC, 17 Non-TRC academic) with HCC over a 15-month period were assessed for Liver reporting and Data System (LI-RADS) guideline compliance. 269 scans (182 CT, 87 MRI) were qualitatively evaluated by 2 independent blinded radiologists for arterial timing, overall image quality, noise and sharpness, with quantification of interobserver variability. The contrast enhancement ratio (CER) for the largest HCC on each scan was calculated using pre- and post-contrast images. Results: 103/104 (99%) of TRC and 44/78 (56%) of CH CTs adhered to LI–RADS imaging guidelines (P < 0.0001). Lack of delayed phase accounted for 32/34 (94%) of noncompliant CH CTs. Regarding MRI, 19/19 (100%) of TRC and 60/68 (88%) of CH scans were adherent (P = 0.12). For both modalities, overall image quality, noise and sharpness were rated significantly higher for TRC than CH. There was moderate interobserver agreement with intraclass correlation coefficient of 0.73, 0.70 and 0.63, respectively. Arterial-phase timing was rated adequate for CT in 75/104 TRC (72%) and 10/68 (14%) CH scans (P < 0.0001) and for MRI in 8/19 (42%) TRC and 23/68 (33%) CH scans (P = 0.17). The CER was significantly higher for TRC versus CH (2.9 vs. 1.9, P < 0.001) and MRI (0.9 vs. 0.7, P = 0.03). Conclusions: Community hospital HCC diagnostic scans significantly lag in critical quality parameters of tumor enhancement, arterial phase timing, perceived image quality, and LI-RADS CT technique compliance compared to a TRC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Application of unsupervised deep learning to image segmentation and in-situ contact angle measurements in a CO 2 -water-rock system

Rock surface wettability is a critical property that regulates multiphase flows in porous media, which can be quantified using the surface contact angle (CA). X-ray micro-computed tomography (μCT) provides an effective approach to in-situ measurements of surface CAs. However, the CA measurement accuracy depends significantly on the quality of CT image segmentation, which is the clustering of CT pixels into separate phases. Inspired by this, we developed a deep learning (DL)-based CA measurement workflow. Motivated by the recent tremendous progress in unsupervised learning techniques and aiming to avoid expensive manual data annotations, an unsupervised DL pipeline for CT image segmentation was proposed and implemented, which includes unsupervised model training and post-processing. The unsupervised model training was driven by a novel loss function constrained with feature similarity and spatial continuity and implemented by iterative forward and backward paths; the former clustered the pixel-wise feature vectors extracted by convolution neural networks, whereas the latter updated the parameters using gradient descent. An over-segmentation strategy was adopted for model training. The post-processing steps based on agglomerative hierarchical clustering (AHC) were implemented to further merge the over-segmented model output to the desired cluster number, which is intended to improve the efficiency of image segmentation. The developed unsupervised DL pipeline was compared with other commonly-used image segmentation methods using pixel-wise and physics-based evaluation metrics on a synthetic raw-image dataset, which had a known ground truth. The unsupervised DL pipeline showed the best performance. Next, the segmented images were input to an automatic CA measurement tool, and the results were validated by comparisons with manual measurements. The CA values from the manual and automatic measurements showed similar distributions and statistical properties. The automatic measurement demonstrated a wider spectrum because of the much larger number of measurement data points. The primary novelty of the unsupervised DL pipeline developed in this study lies in the novel loss function and the over-segmentation strategy associated with AHC post-processing. Finally, the workflow has been proven an efficient tool for pore-scale wettability characterization, which has a wide range of applications in fundamental studies of multiphase flows in natural porous media, which have critical implications to geological carbon sequestration, hydrocarbon energy recovery, and contaminant transport in groundwater.

42 ENGINEERING↗

NeRVI: Compressive neural representation of visualization images for communicating volume visualization results

We present NeRVI, a new deep-learning approach that compresses a large collection of visualization images generated from time-varying data for communicating volume visualization results. Based on an image-based implicit neural representation, our approach represents tens of thousands of high-resolution rendering images parametrized by different parameters via a hybrid model of multilayer perceptrons and convolutional neural networks. Here, our model predicts images and corresponding masks, and the masks are utilized for loss computation and network training to capture fine structural details and small components. In conjunction with model quantization and weight encoding, NeRVI yields highly compact compressive neural representations while preserving the image fidelity well. We demonstrate the effectiveness of NeRVI with isosurface rendering and direct volume rendering images generated from multiple data sets and compare NeRVI with other state-of-the-art deep learning-based (InSituNet, SIREN, NeRF, and NeRV) methods. Quantitative and qualitative results show that NeRVI provides an alternative solution that augments domain scientists' ability to manage, represent, and communicate scientific visualization output.

97 MATHEMATICS AND COMPUTING↗

Two-phase accurate multiplexed structured image capture (2pAc-MUSIC)

Multiplexed Structural Image Capture (MUSIC) technique uses modulation of light from a scene prior to imaging to encode the temporal evolution of target into spatial frequency shifts, with each shift corresponding to a unique time and resulting in individual distinct snapshots. Computational-processing of the multiplexed single-shot image can recover the nanosecond-resolution scene evolution. One of the limitations is the loss of spatial resolution of the recovered image due to limitations of the low-pass spatial frequency filtering depth. Here we demonstrated that two images with complementary spatial phases can be used to enhance the spatial resolutions. For this application, 2 Phase Accurate (2pAc)-MUSIC is implemented that a scene is encoded with two complementary phases. The increased spatial information captured reduces the lower frequency noise in the Fourier domain found in single-phase MUSIC. A recovery algorithm combines the 180-degree spatial frequency shifted images into a single scene and applies a spatial filter in the Fourier domain that has a larger depth than previously possible to achieve a scene with increased spatial resolution. The 2pAc-MUSIC can effectively enhance the spatial resolution by removing the overlapping zero-order spatial frequencies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Visualizing the Three-Dimensional Arrangement of Hydrogen Atoms in Organic Molecules by Coulomb Explosion Imaging

Structure-sensitive methods based on femtosecond light or electron pulses are now making it possible to measure how molecular structures change during light-induced processes. Despite significant progress, high-fidelity imaging of nuclear positions remains a challenge even for relatively small molecular systems and, notably, regarding the positions of hydrogen atoms. As demonstrated in recent work, X-ray-induced Coulomb explosion imaging (CEI) may overcome this obstacle, as its sensitivity does not depend on the mass of the imaged atoms. The photoinduced ring opening of the heterocyclic molecule 2(5 H )-thiophenone has attracted recent interest. Here, in this work, we show that CEI offers a powerful route to imaging the peripheral H atoms in this molecule and thus, more generally, to tracking detailed nuclear motions (e.g., isomerizations) in organic molecules on ultrafast time scales. Specifically, we record momentum-space Coulomb explosion images that report on the three-dimensional positioning of all nuclei within the molecule, for instance, distinguishing H atoms in C–H bonds that lie within or are directed out of the plane defined by the heavy atoms. The prospect of imaging peripheral H atoms to probe photochemical dynamics is explored by coupling ab initio molecular dynamics with classical Coulomb explosion simulations, thereby differentiating potential photoproduct isomers, including those whose structures primarily differ in the position of the hydrogens.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

macroMS: Image-Guided Analysis of Random Objects by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Mass spectrometry imaging is well-suited to characterizing sample surfaces for their chemical content in a spatially resolved manner. However, when the surface contains small objects with significant empty spaces between them, more efficient approaches to sample acquisition are possible. Image-guided mass spectrometry (MS) enables high-throughput analysis of a diverse range of sample types, such as microbial colonies, liquid microdroplets, and others, by recognizing and analyzing selected location targets in an image. Here, we describe an imaging protocol and macroMS, an online software suite that can be used to enhance MS measurements of macroscopic samples that are imaged by a camera or a flatbed scanner. Furthermore, the web-based tool enables users to find and filter targets from the optical images, correct optical distortion issues for improved spatial location of selected targets, input the custom geometry files into an MS device to acquire spectra at the selected locations, and finally, perform limited data analysis and use visualization tools to aid locating samples containing compounds of interest. Using the macroMS suite, an enzyme mutant library of Saccharomyces cerevisiae and nL droplet arrays of Escherichia coli and Pseudomonas fluorescens have been assayed at a rate of ~2 s/sample.

47 OTHER INSTRUMENTATION↗

Scalable 3D reconstruction for X-ray single particle imaging with online machine learning

X-ray free-electron lasers offer unique capabilities for measuring the structure and dynamics of biomolecules, helping us understand the basic building blocks of life. Notably, high-repetition-rate free-electron lasers enable single particle imaging, where individual, weakly scattering biomolecules are imaged under near-physiological conditions with the opportunity to access fleeting states that cannot be captured in cryogenic or crystallized conditions. Existing X-ray single particle reconstruction algorithms, which estimate the particle orientation for each image independently, are slow and memory-intensive when handling the massive datasets generated by emerging free-electron lasers. Here, we introduce X-RAI (X-Ray single particle imaging with Amortized Inference), an online reconstruction framework that estimates the structure of 3D macromolecules from large X-ray single particle datasets. X-RAI consists of a convolutional encoder, which amortizes pose estimation over large datasets, as well as a physics-based decoder, which employs an implicit neural representation to enable high-quality 3D reconstruction in an end-to-end, self-supervised manner. We demonstrate that X-RAI achieves state-of-the-art performance for small-scale datasets in simulation and challenging experimental settings and demonstrate its unprecedented ability to process large datasets containing millions of diffraction images in an online fashion. These abilities signify a paradigm shift in X-ray single particle imaging towards real-time reconstruction.

Computer science↗

Multi-beam X-ray ptychography for high-throughput coherent diffraction imaging

X-ray ptychography is a rapidly developing coherent diffraction imaging technique that provides nanoscale resolution on extended field-of-view. However, the requirement of coherence and the scanning mechanism limit the throughput of ptychographic imaging. Herein, we propose X-ray ptychography using multiple illuminations instead of single illumination in conventional ptychography. Multiple locations of the sample are simultaneously imaged by spatially separated X-ray beams, therefore, the obtained field-of-view in one scan can be enlarged by a factor equal to the number of illuminations. We have demonstrated this technique experimentally using two X-ray beams focused by a house-made Fresnel zone plate array. Two areas of the object and corresponding double illuminations were successfully reconstructed from diffraction patterns acquired in one scan, with image quality similar with those obtained by conventional single-beam ptychography in sequence. Multi-beam ptychography approach increases the imaging speed, providing an efficient way for high-resolution imaging of large extended specimens.

47 OTHER INSTRUMENTATION↗

Energy-resolved neutron imaging and diffraction including grain orientation mapping using event camera technology

Time-of-flight neutron diffraction and energy-resolved imaging each provide unique perspectives into material properties. Neutron diffraction is useful for assessing microstructural parameters such as phase composition, texture, and dislocation densities, though it typically provides averaged data over the sampled volume. Energy-resolved imaging, on the other hand, offers both spatial and spectral information by detecting Bragg edges and neutron absorption resonances, which enables detailed mapping of microstructure and isotopic composition. When combined, these techniques have the potential to enrich our understanding of material behavior across different scales, enhancing our understanding of complex materials. Traditionally, these modalities are conducted on separate instruments, which is time-consuming and poses challenges for data integration. Here, we report the integration of the LumaCam, an event-mode energy-resolved neutron imaging camera with the HIPPO time-of-flight diffractometer at LANSCE. This integration enables simultaneous diffraction and imaging across the full spectrum, with analysis optimized for diffraction and Bragg-edge imaging in the thermal range (0.45–10 Å) and resonance imaging in the epithermal range (0.5–3000 eV), facilitating comprehensive multi-modal analysis. We demonstrate its capabilities through case studies, including spatial mapping of grain orientations in a steel sample and accurate thickness estimations for irregular samples including a depleted uranium cylinder and a natural silver-containing mineral specimen. The combined setup enhances real-time sample alignment and provides comprehensive data for crystal structure, texture, and isotopic composition analysis. This approach opens new possibilities for advanced applications in nuclear engineering, archaeology, and materials science.

36 MATERIALS SCIENCE↗

Image-driven discriminative and generative machine learning algorithms for establishing microstructure–processing relationships

We investigate methods of microstructure representation for the purpose of predicting processing condition from microstructure image data. A binary alloy that is currently under development as a nuclear fuel was studied for the purpose of developing an improved machine learning approach to image recognition, characterization, and building predictive capabilities linking microstructure to processing conditions. Here, we test different microstructure representations and evaluate model performance based on classification accuracy. A classification accuracy of 95.8% was achieved fordistinguishing between micrographs corresponding to ten different thermo-mechanical material processing conditions.We find that our newly developed microstructure representation describes image data well, and the traditional approachof utilizing area fractions of different phases is insufficient for distinguishing between multiple classes using a relativelysmall, imbalanced original data set of 272 images. To explore the applicability of generative methods for supplementing such limited data sets, generative adversarial networks were trained to generate artificial microstructure images. Two different generative networks were trained and tested to assess performance. Challenges and best practices associated with applying machine learning to limited microstructure image data sets is also discussed. Our work has implications for quantitative microstructure analysis, and development of microstructure-processing relationships in limited data sets typical of metallurgical process design studies.

36 MATERIALS SCIENCE↗

Toward implementing autonomous adaptive data acquisition for scanning hyperspectral imaging of biological systems

Autonomous experimentation is an emerging area of research, primarily related to autonomous vehicles, scientific combinatorial discovery approaches in materials science and drug discovery, and iterative research loops of planning, experimentation, and analysis. However, autonomous approaches developed in these contexts are difficult to apply to high-dimensional mapping technologies, such as scanning hyperspectral imaging of biological systems, due to sample complexity and heterogeneity. We briefly cover the history of adaptive sampling algorithms and surrogate modeling in order to define autonomous adaptive data acquisition as an objective-based, flexible building block for future biological imaging experimentation driven by intelligent infrastructure. We subsequently summarize the recent implementations of autonomous adaptive data acquisition (AADA) for scanning hyperspectral imaging, assess how these address the difficulties of autonomous approaches in hyperspectral imaging, and highlight the AADA design variation from a goal-oriented perspective. Finally, we present a modular AADA architecture that embeds AADA-driven flexible building blocks to address the challenge of time resolution for high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems. In our example research-driven experimental design case, we propose an AADA infrastructure for time-resolved, noninvasive, and label-free scanning hyperspectral imaging of living biological systems. This AADA infrastructure can accurately target the correct state of the system for experimental workflows that utilize subsequent expensive, high-information-content analytical techniques.

59 BASIC BIOLOGICAL SCIENCES↗

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.

Engineering↗

Noise from undetected sources in Dark Energy Survey images

ABSTRACT For ground-based optical imaging with current CCD technology, the Poisson fluctuations in source and sky background photon arrivals dominate the noise budget and are readily estimated. Another component of noise, however, is the signal from the undetected population of stars and galaxies. Using injection of artifical galaxies into images, we demonstrate that the measured variance of galaxy moments (used for weak gravitational lensing measurements) in Dark Energy Survey (DES) images is significantly in excess of the Poisson predictions, by up to 30 per cent, and that the background sky levels are overestimated by current software. By cross-correlating distinct images of ‘empty’ sky regions, we establish that there is a significant image noise contribution from undetected static sources (US), which, on average, are mildly resolved at DES resolution. Treating these US as a stationary noise source, we compute a correction to the moment covariance matrix expected from Poisson noise. The corrected covariance matrix matches the moment variances measured on the injected DES images to within 5 per cent. Thus, we have an empirical method to statistically account for US in weak lensing measurements, rather than requiring extremely deep sky simulations. We also find that local sky determinations can remove most of the bias in flux measurements, at a small penalty in additional, but quantifiable, noise.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Detecting optical transients using artificial neural networks and reference images from different surveys

ABSTRACT We present a technique to detect optical transients based on an artificial neural networks method. We describe the architecture of two networks capable of comparing images of the same part of the sky taken by different telescopes. One image corresponds to the epoch in which a potential transient could exist; the other is a reference image of an earlier epoch. We use data obtained by the Dr. Cristina V. Torres Memorial Astronomical Observatory and archival reference images from the Sloan Digital Sky Survey. We trained a convolutional neural network and a dense layer network on simulated source samples and then tested the trained networks on samples created from real image data. Autonomous detection methods replace the standard process of detecting transients, which is normally achieved by source extraction of a difference image followed by human inspection of the detected candidates. Replacing the human inspection component with an entirely autonomous method would allow for a rapid and automatic follow-up of interesting targets of opportunity. The toy-model pipeline that we present here is not yet able to replace human inspection, but it might provide useful hints to identify potential candidates. The method will be further expanded and tested on telescopes participating in the Transient Optical Robotic Observatory of the South Collaboration.

79 ASTRONOMY AND ASTROPHYSICS↗

Experimental study of multiple-orientation muon tomography with image optimization in sparse data environments

Due to the high penetrating power of cosmic-ray muons, they can be used to probe very thick and dense objects. As muons are charged particles, they can be tracked by ionization detectors, determining the position and direction of the muons. With detectors on either side of an object to measure particle direction change, scattering information within the object can be found. This can be used to produce a scattering-intensity image within the object related to density and atomic number. Such imaging is typically performed with a single detector-object orientation, taking advantage of the more intense downward flux of muons, producing planar imaging with some depth-of-field information in the third dimension. Several simulation studies were published with multiorientation tomography, which can form a three-dimensional representation faster than a single-orientation view. In this study, experimental muon-scatter-based tomography was performed using a concrete filled steel drum with several different metal wedges inside, with the drum between detector planes. Data were collected from different detector-object orientations by rotating the steel drum. The data collected from each orientation were combined using two different tomographic methods. A traditional inverse Radon transform approach used for computed tomography and a combination of multiple depth-of-field reconstructions were applied to the data. As cosmic-ray muon flux imaging is rate limited, the imaging techniques were compared for sparse data. Using the combined depth-of-field reconstruction technique, fewer detector-object orientations were needed to reconstruct images that could be used to differentiate the metal wedges.

47 OTHER INSTRUMENTATION↗

Neutron Imaging Using Organic Glass Scintillators

In this work, we develop of a compact neutron imaging system based on organic glass scintillator and silicon photomultiplier arrays. The recently developed organic glass scintillator has excellent neutron and gamma-ray detection efficiency and exhibits pulse shape discrimination capability that is nearly as good as current state-of-the-art materials such as trans-stilbene. We have cast and characterized 6 mm by 6 mm by 50 mm bars of organic glass in our laboratory. When coupled to a silicon photomultiplier array, these bars demonstrated better energy and timing resolution than the stilbene organic scintillator. Here, this performance makes organic glass an ideal material for a compact neutron imaging system, which must resolve neutron scatter events on a sub-nanosecond time scale. We have demonstrated neutron imaging with bars of organic glass scintillator coupled to arrays of silicon photomultipliers. Additional bars of organic glass will be implemented into the system to improve the efficiency and imaging performance. The resulting system will be demonstrated using 252 Cf and PuBe neutron sources in our laboratory. In addition, we will compare imaging performance to other compact neutron imaging systems that exist in literature.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗