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At least 55 records · Page 3

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.

Narciso, Diogo A. C. (ORCID:0000000227767477)↗

Monochromatic imaging instrumentation for applications in aeronomy of the earth and planets

Monochromatic imaging instrumentation has been developed that uses narrow-band (12 A FWHP) interference filters or plane reflection gratings for 2D imaging and imaging spectrograph applications. By changing the optics in front of the filter or grating, the field of view of the instruments can be varied from 180 deg to 6 deg. In the case of the 2D monochromatic imager, the 12 mm-diameter filtered image is formed at about f/1 on the input photocathode of an intensified CCD camera (380 x 488 pixels). The sensitivities of the systems are about 50-100 R s (S/N about 2). Examples of data taken with both of these instruments include detection and mapping of Jupiter's sodium magnetonebula and stable auroral red arcs in the terrestrial ionosphere.

Baumgardner, Jeffrey↗

3D Observation of GEMS by Electron Tomography

Amorphous silicates in chondritic porous interplanetary dust particles (CP-IDPs) coming from comets are dominated by glass with embedded metal and sulfides (GEMS). GEMS grains are submicron-sized rounded objects (typically 100-500) nm in diameter) with anaometer-sized (10-50 nm) Fe-Ni metal and sulfide grains embedded in an amorphous silicate matrix. Several formation processes for GEMS grains have been proposed so far, but these models are still being debated [2-5]. Bradley et al. proposed that GEMS grains are interstellar silicate dust that survived various metamorphism or alteration processes in the protoplanetary disk and that they are amorphiation products of crystalline silicates in the interstellar medium by sputter-deposition of cosmic ray irradiation, similar to space weathering [2,4]. This consideration is based on the observation of nano-sized crystals (approximately 10 nm) called relict grains in GEMS grains and their shapes are pseudomorphs to the host GEMS grains. On the other hand, Keller and Messenger proposed that most GEMS formed in the protoplanetary disk as condensates from high temperature gas [3,5]. This model is based on the fact that most GEMS grains have solar isotopic compositions and have extremely heterogeneous and non-solar elemental compositions. Keller and Messenger (2011) also reported that amorphous silicates in GEMS grains are surrounded by sulfide grains, which formed as sulfidization of metallic iron grains located on the GEMS surface. The previous studies were performed with 2D observation by using transmission electron microscopy (TEM) or scanning TEM (STEM). In order to understand the structure of GEMS grains described above more clearly, we observed 3D structure of GEMS grains by electron tomography using a TEM/STEM (JEM-2100F, JEOL) at Kyoto University. Electron tomography gives not only 3D structures but also gives higher spatial resolution (approximately a few nm) than that in conventional 2D image, which is restricted by sample thickness ) approx. or greater than 50 nm). Three cluster IDPs (L2036AA5 cluster4, L2009L8 cluster 13 and W726A2) were used for the observations. ID W726A2 was collected without silicon oil, which is ordinary used to collect IDPs, so this sample has no possibility of contaminations caused by silicon oil or solvent to rinse it [6]. The samples were embedded in epoxy risin and sliced into ultrathin sections (50-300 nm) using an ultramicotome. The sections were observed by BF-TEM and HAADF-STEM (high angle annular dark field-scanning TEM) modes. Images were obtained by rotating the sample tilt angle over a range of +/- 65 deg in 1 deg steps. The obtained images were reconstructed to slice images. Mineral phases in the slice images were estimated by comparing with a 2D elemental map obtained by an EDS (energy dispersive X-ray spectroscopy) system equipped in the TEM/STEM. Careful examination of the slice images confirmed that iron grains are embedded in the amorphous silicate matrix of the GEMS grains, but sulfide grains were mainly present on the surface of the amorphous silicate. These results are consistent with the model that GEMS grains formed as condensates [3,5], although more data are needed to conclude the origin of GEMS grains. The present study is the first successful example adapting the electron tomography to the IDPs. This type of analysis will be important for planetary material sciences in the future.

Matsuno, Junya↗

Upgrades to the gamma ray imager on DIII-D enabling access to high flux hard x-ray measurements during the runaway electron plateau phase (invited)

The Gamma Ray Imager (GRI) is a pinhole camera providing 2D imaging of MeV hard x-ray (HXR) bremsstrahlung emission from runaway electrons (REs) over the poloidal cross section of the DIII-D tokamak. We report a series of upgrades to the GRI expanding the access to RE scenarios from the diagnosis of a trace amount of REs to high flux HXR measurements during the RE plateau phase. We present the implementation of novel gamma ray detectors based on LYSO and YAP crystals coupled to multi-pixel photon counters, enabling a count rate in excess of 1 MHz. Finally, we highlight new insights into the RE physics discovered during the current quench and RE plateau phase experiments as the result of these upgrades.

Lvovskiy, A. (ORCID:0000000236491169)↗

3D Source Reconstruction Using Coded Aperture Gamma-Ray Imaging

Recent measurements with coded-aperture imagers demonstrate material mass determination in a holdup setting to an accuracy within a few percent. This capability is of particular interest to the Surplus Plutonium Disposition (SPD) project, which aims to dilute and dispose of surplus plutonium oxide. Gamma-ray imagers can be used to determine holdup without interrupting normal operations. In this work, we examine techniques for 3D source localization and mass determination using gamma-ray imagers. Coded-aperture imagers provide excellent source localization within the 2D image plane; however, multiple imagers operating in tandem are necessary to identify source location in 3D space. A Maximum Likelihood Expectation-Maximization (MLEM) method for fitting detector mappings is a powerful tool for accomplishing this task. MLEM allows 3D source localization to be simultaneously constrained using multiple gamma-ray imagers by constructing the basis for the MLEM fit using detector mappings from different detector locations stitched together. Each of these basis points represents a singular response from a source in 3D space and is generated using Monte Carlo simulations of sources placed individually at different locations throughout the imager’s field of view. Additionally, implementing knowledge of the physical equipment in the simulations of the glovebox used for the SPD project incorporates attenuation effects that are needed to calculate material holdup.

Laminack, Alex↗

TPSAS-NF1676L-33668-DND

A three-color pyrometer has been developed based on plenoptic imaging technology. Three bandpass filters placed in front of the camera lens allows separate 2D images to be obtained at three different wavelengths. Images were obtained of different black- or grey-bodies including a calibration furnace, a radiation heater, a sooting butane flame and a luminous sulfur match flame. The images were processed to determine 2D temperature distributions. Calibration results in the furnace showed that the instrument could measure temperature with an accuracy and precision of 10 Kelvins between 1100 and 1350 K. Time-resolved 2D measurements of the radiation heater, flame and match are shown.

Paul M Danehy↗

Characterization of a Low-Temperature Plasma (LTP) Ambient Ionization Source Using Temporally Resolved Monochromatic Imaging Spectrometry

The low-temperature plasma (LTP) probe is a common plasma-based source used for ambient desorption–ionization mass spectrometry (MS). While the LTP probe has been characterized in detail with MS, relatively few studies have used optical spectroscopy. In this paper, two-dimensional (2D) imaging at selected wavelengths is used to visualize important species in the LTP plasma jet. First, 2D steady-state images of the LTP plume for N 2 + (391.2 nm), He I (706.5 nm), and N 2 (337.1 nm) emissions were recorded under selected plasma conditions. Second, time-resolved 2D emission maps of radiative species in the LTP plasma jet were recorded through the use of a 200 ns detection gate and varying gate delays with respect to the LTP trigger pulse. Emission from He I, N 2 + , and N 2 in the plasma jet region was found to show a transient behavior (often referred to as plasma bullets) lasting only a few microseconds. The N 2 + and He I maps were highly correlated in spatial and temporal structure. Further, emission from N 2 showed two maxima in time, one before and one after the maximum emission for N 2 + and He I, due to an initial electronic excitation wave and ion–electron recombination, respectively. Third, the interaction of the LTP probe with a sample substrate and an electrically grounded metallic needle was studied. Emission from a fluorophore on the sample substrate showed an initial photon-induced excitation from plasma-generated photons followed by electronic excitation by other plasma species. The presence of a grounded needle near the plasma jet significantly extended the plasma jet lifetime and also generated a long-lived corona discharge on the needle. The effect of LTP operating parameters on emission spectra was correlated with mass-spectral results including reagent-ion signals. Lastly, five movies provide a side-by-side comparison of the temporal behavior of emitting species and insights into the interactions of the emission clouds with a sample surface as well as an external needle. Temporally and spatially resolved imaging provided insights into important processes in the LTP plasma jet, which will help improve analyte ion sampling in LTP–MS.

Chan, George C. -Y.↗

Phase-Conjugate Receiver for Gaussian-State Quantum Illumination

An active optical sensor probes a region of free space that is engulfed in bright thermal noise to determine the presence (or absence) of a weakly reflecting target. The returned light (which is just thermal noise if no target is present, and thermal noise plus a weak reflection of the probe beam if a target is present) is measured and processed by a receiver and a decision is made on whether a target is present. It has been shown that generating an entangled pair of photons (which is a highly nonclassical state of light), using one photon as the probe beam and storing the other photon for comparison to the returned light, has superior performance to the traditional classical-light (coherent-state) target detection sensors. An entangled-photon transmitter and optimal receiver combination can yield up to a factor of 4 (i.e., 6 dB) gain in the error-probability exponent over a coherent state transmitter and optimal receiver combination, in a highly lossy and noisy scenario (when both sensors have the same number of transmitted photons). However, the receiver that achieves this advantage is not known. One structured receiver can close half of the 6-dB gap (i.e., a 3-dB improvement). It is based on phase-conjugating the returned light, then performing dual-balanced difference detection with the stored half of the entangled-photon pair. Active optical sensors are of tremendous value to NASA s missions. Although this work focuses on target detection, it can be extended to imaging (2D, 3D, hyperspectral, etc.) scenarios as well, where the image quality can be better than that offered by traditional active sensors. Although the current work is theoretical, NASA s future missions could benefit significantly from developing and demonstrating this capability. This is an optical receiver design whose components are, in principle, all implementable. However, the work is currently entirely theoretical. It is necessary to: 1. Demonstrate a bench-top proof of the theoretical principle, 2. Create an operational prototype off-the-bench, and 3. Build a practical sensor that can fly in a mission.

Erkmen, Baris I.↗

A VR-based volumetric medical image segmentation and visualization system with natural human interaction

Volume rendering produces informative two-dimensional (2D) images from a 3-dimensional (3D) volume. It highlights the region of interest and facilitates a good comprehension of the entire data set. However, volume rendering faces a few challenges. First, a high-dimensional transfer function is usually required to differentiate the target from its neighboring objects with subtle variance. Unfortunately, designing such a transfer function is a strenuously trial-and-error process. Second, manipulating/visualizing a 3D volume with a traditional 2D input/output device suffers dimensional limitations. To address all the challenges, we design NUI-VR 2 , a natural user interface-enabled volume rendering system in the virtual reality space. NUI-VR 2 marries volume rendering and interactive image segmentation. It transforms the original volume into a probability map with image segmentation. A simple linear transfer function will highlight the target well in the probability map. More importantly, we set the entire image segmentation and volume rendering pipeline in an immersive virtual reality environment with a natural user interface. NUI-VR 2 eliminates the dimensional limitations in manipulating and perceiving 3D volumes and dramatically improves the user experience.

42 ENGINEERING↗

Biases associated with a particular image volume metric

Image analysis area and volume metrics A 80 and V 80 , used by others, are studied as a function of image morphology, a 3D feature, and Monte Carlo noise in simulated images. The A 80 area metric is found to be stable, with consistent results (and meaning) obtainable without a detailed understanding of 3D features and/or simulation noise levels. However, the V 80 volume metric varies significantly with image morphology, 3D features, and simulation noise. If an experimental image set gives A 80 area inferences that are consistent with 2D image simulations, but V 80 volume inferences that are significantly larger than those corresponding to simulated images, then issues related to 3D features and simulation noise should be explored before conclusions are drawn related to a possible mismatch in the real physical size of experimental and simulated source volumes.

47 OTHER INSTRUMENTATION↗

A Plenoptic Multi-Color Imaging Pyrometer

A three-color pyrometer has been developed based on plenoptic imaging technology. Three bandpass filters placed in front of a camera lens allow separate 2D images to be obtained on a single image sensor at three different and adjustable wavelengths selected by the user. Images were obtained of different black- or grey-bodies including a calibration furnace, a radiation heater, and a luminous sulfur match flame. The images obtained of the calibration furnace and radiation heater were processed to determine 2D temperature distributions. Calibration results in the furnace showed that the instrument can measure temperature with an accuracy and precision of 10 Kelvins between 1100 and 1350 K. Time-resolved 2D temperature measurements of the radiation heater are shown.

Danehy, Paul M.↗

Bayesian inference in band excitation scanning probe microscopy for optimal dynamic model selection in imaging

The universal tendency in scanning probe microscopy (SPM) over the last two decades is to transition from simple 2D imaging to complex detection and spectroscopic imaging modes. The emergence of complex SPM engines brings forth the challenge of reliable data interpretation, i.e., conversion from detected signals to descriptors specific to tip–surface interactions and subsequently to material’s properties. In this work, we implemented a Bayesian inference approach for the analysis of the image formation mechanisms in band excitation SPM. Compared to the point estimates in classical functional fit approaches, Bayesian inference allows for the incorporation of extant knowledge of materials and probe behavior in the form of corresponding prior distribution and return the information on the material functionality in the form of readily interpretable posterior distributions. We explore the nonlinear mechanical behaviors spatially in a classical ferroelectric material, PbTiO 3 . We observe the non-trivial evolution of the Duffing stiffness term and the nonlinearity of the sample surface, determine spatial clustering of the nonlinear response, and perform a Landau analysis on predicting the nonlinear coefficient, which indicates that ferroelectric behavior can be a cause of the observed results. These observations suggest that the spectrum of anomalous behaviors at the ferroelectric domain walls may be broader than previously believed and can extend to non-conventional mechanical properties in addition to static and microwave conductance.

36 MATERIALS SCIENCE↗

Creating ground truth for nanocrystal morphology: a fully automated pipeline for unbiased transmission electron microscopy analysis

Control over colloidal nanocrystal morphology (size, size distribution, and shape) is important for tailoring the functionality of individual nanocrystals and their ensemble behavior. Despite this, traditional methods to quantify nanocrystal morphology are laborious. New developments in automated morphology classification will accelerate these analyses but the assessment of machine learning models is limited by human accuracy for ground truth, causing even unsupervised machine learning models to have inherent bias. Herein, we introduce synthetic image rendering to solve the ground truth problem of nanocrystal morphology classification. By simulating 2D images of nanocrystal shapes via a function of high-dimensional parameter space, we trained a convolutional neural network to link unique morphologies to their simulated parameters, defining nanocrystal morphology quantitatively rather than qualitatively. An automated pipeline then processes, quantitatively defines, and classifies nanocrystal morphology from experimental transmission electron microscopy (TEM) images. Using improved computer vision techniques, 42,650 nanocrystals were identified, assessed, and labeled with quantitative parameters, offering a 600-fold improvement in efficiency over best-practice manual measurements. Further, a classification algorithm was trained with a prediction accuracy of 99.5%, which can successfully analyze a range of concave, convex, and irregular nanocrystal shapes. The resulting pipeline was applied to differentiating two syntheses of nominally cuboidal CsPbBr 3 nanocrystals and uniquely classifying binary nickel sulfide nanocrystal phase based on morphology. This pipeline provides a simple, efficient, and unbiased method to quantify nanocrystal morphology and represents a practical route to construct large datasets with an absolute ground truth for training unbiased morphology-based machine learning algorithms.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Compact Midwave Imaging System: Results from an Airborne Demonstration

The Compact Midwave Imaging System (CMIS) is a wide field of view, multi-angle, multi-spectral push frame imager that relies on the forward motion of the satellite to create a two-dimensional (2D) image swath. An airborne demonstration of CMIS was successfully completed in January-February 2021 on the NASA Langley Research Center Gulfstream III. The primary objective of the four-flight campaign was to demonstrate the capability of this unique instrument to perform stereo observations of clouds and other particulates (e.g. smoke) in the atmosphere. It is shown that the midwave infrared (MWIR) spectral bands of CMIS provide a unique 24/7 capability with high resolution for accurate stereo sensing.The instrument relies on new focal plane array (FPA) technology, which provides excellent sensitivity at much warmer detector temperatures than traditional technologies. This capability enabled a compact, low-cost design that can provide atmospheric motion vectors and cloud heights to support requirements for atmospheric winds in the 2017-2027 Earth Science Decadal Survey. Applications include day/night observations of the planetary boundary layer, severe weather, and wildfires. A comparison with current space-based earth science instruments demonstrates that the SWIR/MWIR multi-spectral capability of CMIS is competitive with larger, more expensive instrumentation. Imagery obtained over a controlled burn and operating nuclear power plant demonstrated the sensitivity of the instrument to temperature variations. The system relies on a mature stereoscopic imaging technique applied to the same scene from two independent platforms to unambiguously retrieve atmospheric motion vectors (AMVs) with accurate height assignment.This capability has been successfully applied to geostationary and low-earth orbit satellites to achieve excellent accuracy. When applied to a ground-point validation case, the accuracy for the CMIS aircraft observations was 20 m and 0.3 m/s for cloud heights and motion vectors, respectively. This result was confirmed by a detailed error analysis with analytical and covariance models. The results for CMIS cases with under flights of Aeolus, CALIPSO and Aqua provided a good validation of expected accuracies. The paper also showed the feasibility of accommodating CMIS on CubeSats to enable multiple instruments to be flown in a leader-follower mode.

stereo winds↗

DeepPatent2: A Large-Scale Benchmarking Corpus for Technical Drawing Understanding

Abstract Recent advances in computer vision (CV) and natural language processing have been driven by exploiting big data on practical applications. However, these research fields are still limited by the sheer volume, versatility, and diversity of the available datasets. CV tasks, such as image captioning, which has primarily been carried out on natural images, still struggle to produce accurate and meaningful captions on sketched images often included in scientific and technical documents. The advancement of other tasks such as 3D reconstruction from 2D images requires larger datasets with multiple viewpoints. We introduce DeepPatent2, a large-scale dataset, providing more than 2.7 million technical drawings with 132,890 object names and 22,394 viewpoints extracted from 14 years of US design patent documents. We demonstrate the usefulness of DeepPatent2 with conceptual captioning. We further provide the potential usefulness of our dataset to facilitate other research areas such as 3D image reconstruction and image retrieval.

97 MATHEMATICS AND COMPUTING↗

py4DSTEM: A Software Package for Four-Dimensional Scanning Transmission Electron Microscopy Data Analysis

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full two-dimensional (2D) image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields, and other sample-dependent properties. However, extracting this information requires complex analysis pipelines that include data wrangling, calibration, analysis, and visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open-source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail and present results from several experimental datasets. We also implement a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open-source HDF5 standard. We hope this tool will benefit the research community and help improve the standards for data and computational methods in electron microscopy, and we invite the community to contribute to this ongoing project.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Imaging the 3.4-micron feature in Comet Levy (1990c)

The IRTF's ProtoCAM has been used to observe the organic emission feature peaking near 3.36 microns in Comet Levy. 2D images of the spatial distribution of the 3.4-micron organic emission exhibit brightness profiles statistically indistinguishable from that of the dust continuum, within 1225 of the cometary nucleus; this suggests a progenitor for the emission feature which is not a photodissociation fragment of some other species.

Klavetter, James J.↗

4D Light Field Imaging System Using Programmable Aperture

Complete depth information can be extracted from analyzing all angles of light rays emanated from a source. However, this angular information is lost in a typical 2D imaging system. In order to record this information, a standard stereo imaging system uses two cameras to obtain information from two view angles. Sometimes, more cameras are used to obtain information from more angles. However, a 4D light field imaging technique can achieve this multiple-camera effect through a single-lens camera. Two methods are available for this: one using a microlens array, and the other using a moving aperture. The moving-aperture method can obtain more complete stereo information. The existing literature suggests a modified liquid crystal panel [LC (liquid crystal) panel, similar to ones commonly used in the display industry] to achieve a moving aperture. However, LC panels cannot withstand harsh environments and are not qualified for spaceflight. In this regard, different hardware is proposed for the moving aperture. A digital micromirror device (DMD) will replace the liquid crystal. This will be qualified for harsh environments for the 4D light field imaging. This will enable an imager to record near-complete stereo information. The approach to building a proof-ofconcept is using existing, or slightly modified, off-the-shelf components. An SLR (single-lens reflex) lens system, which typically has a large aperture for fast imaging, will be modified. The lens system will be arranged so that DMD can be integrated. The shape of aperture will be programmed for single-viewpoint imaging, multiple-viewpoint imaging, and coded aperture imaging. The novelty lies in using a DMD instead of a LC panel to move the apertures for 4D light field imaging. The DMD uses reflecting mirrors, so any light transmission lost (which would be expected from the LC panel) will be minimal. Also, the MEMS-based DMD can withstand higher temperature and pressure fluctuation than a LC panel can. Robotics need near complete stereo images for their autonomous navigation, manipulation, and depth approximation. The imaging system can provide visual feedback

Bae, Youngsam↗