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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

FLIMJ: An open-source ImageJ toolkit for fluorescence lifetime image data analysis

In the field of fluorescence microscopy, there is continued demand for dynamic technologies that can exploit the complete information from every pixel of an image. One imaging technique with proven ability for yielding additional information from fluorescence imaging is Fluorescence Lifetime Imaging Microscopy (FLIM). FLIM allows for the measurement of how long a fluorophore stays in an excited energy state, and this measurement is affected by changes in its chemical microenvironment, such as proximity to other fluorophores, pH, and hydrophobic regions. This ability to provide information about the microenvironment has made FLIM a powerful tool for cellular imaging studies ranging from metabolic measurement to measuring distances between proteins. The increased use of FLIM has necessitated the development of computational tools for integrating FLIM analysis with image and data processing. To address this need, we have created FLIMJ, an ImageJ plugin and toolkit that allows for easy use and development of extensible image analysis workflows with FLIM data. Built on the FLIMLib decay curve fitting library and the ImageJ Ops framework, FLIMJ offers FLIM fitting routines with seamless integration with many other ImageJ components, and the ability to be extended to create complex FLIM analysis workflows. Building on ImageJ Ops also enables FLIMJ’s routines to be used with Jupyter notebooks and integrate naturally with science-friendly programming in, e.g., Python and Groovy. We show the extensibility of FLIMJ in two analysis scenarios: lifetime-based image segmentation and image colocalization. We also validate the fitting routines by comparing them against industry FLIM analysis standards.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

nsCamera ImageJ Plugin

ImageJ plugin used to run hCMOS via the Python nsCamera library. The Python nsCamera has already been open-sourced under CP02612

Hill, Jeremy↗
DOE OSTI2022

Real-time image denoising of mixed Poisson–Gaussian noise in fluorescence microscopy images using ImageJ

Fluorescence microscopy imaging speed is fundamentally limited by the measurement signal-to-noise ratio (SNR). To improve image SNR for a given image acquisition rate, computational denoising techniques can be used to suppress noise. However, common techniques to estimate a denoised image from a single frame either are computationally expensive or rely on simple noise statistical models. These models assume Poisson or Gaussian noise statistics, which are not appropriate for many fluorescence microscopy applications that contain quantum shot noise and electronic Johnson–Nyquist noise, therefore a mixture of Poisson and Gaussian noise. In this paper, we show convolutional neural networks (CNNs) trained on mixed Poisson and Gaussian noise images to overcome the limitations of existing image denoising methods. The trained CNN is presented as an open-source ImageJ plugin that performs real-time image denoising (within tens of milliseconds) with superior performance (SNR improvement) compared to conventional fluorescence microscopy denoising methods. The method is validated on external datasets with out-of-distribution noise, contrast, structure, and imaging modalities from the training data and consistently achieves high-performance ( > <#comment/> 8 d B ) denoising in less time than other fluorescence microscopy denoising methods.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Adhesion Capabilities of Permanent Foaming Fixatives

DOE-EM have identified an operational requirement for a fixative that can immobilize and/or encapsulate residual contamination in 3D void volumes (pipes, gloveboxes, waste containers, etc.) during D and D activities. Failure to safely and effectively immobilize residual contamination can: Put workers at risk; Contaminate the public and environment; Drive up costs. Commercial-off-the-shelf (COTS) polyurethane (PU) foams is one possible solution and is currently being investigated by Savannah River National Lab (SRNL). Adhesion testing will dictate how well PU foams will adhere and immobilize residual contamination onto a substrate. Results can provide a performance criteria for Section 5 of ASTM E3191: Standard Specification for Permanent Foaming Fixatives Used to Mitigate Spread of Radioactive Contamination. Initial mechanical testing showed intumescent rigid PU foams were best in class (tensile, compression, TGA/DSC) Application of intumescent rigid PU foam in pipe scenario with 'contamination' showed excellent adhesion capabilities as long as foam had contact with pipe. The foam, however, was not able to penetrate 'contamination' but created pockets where the contamination interacted with the substrate. Pretreatment options of pipe were considered to produce better immobilization capabilities. Pretreatment options included COTS products like baking spray, rubber cement, and soap. Foam was still able to immobilize on a global sense, but not a local sense. Essentially acted as a mechanical plug. A tensile tester (MTS Criterion Series 43) was utilized to evaluate the tensile adhesion strength of 6 COTS PU foams. ASTM D1623: Tensile and Tensile Adhesion Properties of Rigid Cellular Plastics. Procedures: PU foams were cured between two smooth 2'' x 2'' 304 stainless steel coupons with hinges glued on plates for gripping support. Parameters Used: Pull rate of 0.1 in/min. Calculations: Tensile adhesion strength, elongation, and ImageJ analysis of how PU foam is left on substrate. Outcome: The PU foam with the best adhesion capabilities would be downselected for further evaluation to be used as a permanent foaming fixative. The rigid PU foams had the best adhesion capabilities with the R1 foam having a max load of 236 N. One of the I-R2 samples reached almost 450 N and another sample reached 2500 N before slipping. The other intumescent foam, I-F4, had the most coverage on the stainless steel coupon's surface from the ImageJ results (61.43% surface coverage). The intumescent foam, I-R2, will be the foam of choice for future testing due its fire retardant and adhesion capabilities. Future directions: Conduct the following experiment in a pipe scenario with the down-selected PU foam. Procedures: PU foam will be cured between in a 304 stainless steel pipe (ID: 4'', OD: 4.5'', Height: 4''). Parameters Used: Compression testing results will be referenced to determine if foam's adhesion strength would be greater its compression strength as its being compressed. Calculations: Compression strength, shear stress, total time elapsed. Conduct further adhesion testing with the down-selected PU foam (I-R2) to be treated as a permanent foaming fixative (PFF). Determine the minimum contact the PFF should have with the substrate for adequate results. Evaluate if PFF's adhesion capabilities is time dependent (3.1.5 of ASTM E3911). Subject PFF to seismic stressors addressed in Safety Basis of Interim Operation documents (SBIO) to further evaluate adhesion capabilities.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Analysis of the Surface Morphology and Chemical Composition of Zr-Nb3Sn Alloys with Different Zr Concentrations

In the field of superconducting science, Nb has been the material of choice for Radio Frequency (RF) Cavities for years. However, in recent years Nb3Sn has shown to be a promising alternative to Nb. Its combination of a significantly high superconducting transition temperature and a much higher value of upper critical magnetic field (Hc2), has been the reason the alloy has been so widely studied. This project aims to develop materials to further improve the high magnetic field performance of Nb3Sn by improving its upper critical magnetic field and critical current density (Jc). One way to improve the Jc and the Hc2 is to create more grain boundaries in the Nb3Sn alloy allowing them to trap more magnetic flux lines in the materials. To do this the grains must be made smaller which will naturally cause the formation of more grain boundaries. A common way to create smaller grains is by doping an impurity in the alloy. In this study, Nb3Sn was doped with Zr to form Zr-Nb3Sn alloys. This project investigates the surface properties and chemical composition of Zr-Nb3Sn alloys with varying zirconium concentrations (~0.5% and ~24% Zr). Using Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS), and X-ray Photoemission Spectroscopy (XPS), allowed for the characterization of the differences in surface morphology and elemental composition between samples. SEM images were quantified using ImageJ giving insight into grain distribution. The results indicate that increased Zr concentration creates smaller grains in the Zr-Nb3Sn alloy. Furthermore, the ~ 24% Zr grew nanoscale particles on the surface that are possible oxides. XPS data revealed that as Zr concentration increased, the total Nb oxides (NbOx) thickness decreased. Conversely, as Zr concentration increased, the surface Sn oxides (SnOx) also increased slightly. Quantification via ImageJ of SEM data showed that the ~ 0.5% Zr sample had a grain size of ~ 5300 nm2. These results show that Zr inclusion leads to smaller grain formations, which is promising in the world of superconducting RF cavities for high magnetic field applications.

Sue, Micah↗
DOE OSTI2022

A New Workflow of X-ray CT Image Processing and Data Analysis of Structural Features in Rock Using Open-Source Software

X-ray computed tomography (CT) images of rock specimens often contain artifacts which must be corrected before scientific analyses are performed. Here, we present a new workflow of automated image processing to utilize poor-quality X-ray CT scan images. The workflow runs on the open-source image analysis software and efficiently separates desired features from low-contrast scanned images. The new workflow is a two-step technique using contrast enhancement and automated feature segmentation to generate noise-free binary images. The results of binary images using the proposed workflow and using a conventional thresholding technique are analyzed to show the quality of the proposed method. The paper also presents a workflow of estimating the structural geometries of features in two and three dimensions. The results of the structural feature analyses and computational time were compared between the open-source (ImageJ) and commercial image analysis software (Bruker Computed Tomography Analyzer). The commercial software was more computationally efficient, but the task-specific macros in open-source software enabled the user-desired automation in image processing and data extraction of desired structural features of comparable quality.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Variability and associated uncertainty in image analysis for soiling characterization in solar energy systems

The accumulation of soiling on photovoltaic modules and on the mirrors of concentrating solar power systems causes non-negligible energy losses with economic consequences. These challenges can be mitigated, or even prevented, through appropriate actions if the magnitude of soiling is known. Particle counting analysis is a common procedure to characterize soiling, as it can be easily performed on micrographs of glass coupons or solar devices that have been exposed to the environment. Particle counting does not, however, yield invariant results across institutions. The particle size distribution analysis is affected by the operator of the image analysis software and the methodology utilized. The results of a round-robin study are presented in this work to explore and elucidate the uncertainty related to particle counting and its effect on the characterization of the soiling of glass surfaces used in solar energy conversion systems. An international group of soiling experts analyzed the same 8 micrographs using the same open-source ImageJ software package. The variation in the particle analyses results were investigated to identify specimen characteristics with the lowest coefficient of variation (CV) and the least uncertainty among the various operators. The mean particle diameter showed the lowest CV among the investigated characteristics, whereas the number of particles exhibited the largest CV. Additional parameters, such as the fractional area coverage by particles and parameters related to the distribution's shape yielded intermediate CV values. These results can provide insights on the magnitude inter-lab variability and uncertainty for optical and microscope-based soiling monitoring and characterization.

14 SOLAR ENERGY↗
DOE OSTI2024

"Soiling, Cleaning, and Abrasion: The Results of the Five-Year Photovoltaic Glass Coating Field Study" [Slides]

External contamination ("soiling") of the incident surface is a major limiting factor for solar technologies. A 5-year field glass coupon study was conducted to better understand external contamination and its effects; compare cleaning methods and the use of preventative coatings; and explore the abrasion resulting from cleaning to advise on accelerated abrasion testing. Test sites included the cities of Dubai (UAE), Kuwait City (Kuwait), Mesa (AZ), Mumbai (India), and Sacramento (CA). Through the 5-year cumulative study, dry brush, water spray, and wet sponge and squeegee cleaning methods were compared to no cleaning. Optical microscopy was used to obtain images, including representative color images, grayscale images for object analysis, and oblique images for coating integrity assessment. A thresholding protocol was developed to analyze and distinguish specimens using the ImageJ software. Optical performance was quantified using a spectrophotometer, including comprehensive optical characterization (transmittance, reflectance, and absorptance in addition to forward- and back-scattering). Atomic force microscopy was used to verify the abrasion damage morphology, including the width and depth of surface scratches. Analysis of the results included correlation of optical performance and particle area coverage, rank order (by coating or location), and the acceleration factor for abrasion damage. The efficacy of external cleaning was more readily distinguished from the effectiveness of antisoiling coatings. The acceleration factor for dry brush cleaning of a porous silica coating was found to be on the order of unity.

14 SOLAR ENERGY↗
DOE OSTI2024

Seed classification with random forest models

Premise: To improve forest conservation monitoring, we developed a protocol to automatically count and identify the seeds of plant species with minimal resource requirements, making the process more efficient and less dependent on human operators. Methods and Results: Seeds from six North American conifer tree species were separated from leaf litter and imaged on a flatbed scanner. In the most successful species-classification approach, an ImageJ macro automatically extracted measurements for random forest classification in the software R. The method allows for good classification accuracy, and the same process can be used to train the model on other species. Conclusions: This protocol is an adaptable tool for efficient and consistent identification of seed species or potentially other objects. Automated seed classification is efficient and inexpensive, making it a practical solution that enhances the feasibility of large-scale monitoring projects in conservation biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Development of Parameters for the Particle Size Distribution of TATB

Laser light scattering (LLS), manual counting of scanning electron microscopy (SEM) images, and reduction of SEM images using ImageJ (open source program) to determine Feret (caliper) diameters were applied to determine particle size distribution (PSD) of four preparations of 1,3,5‐triamino‐2,4,6‐trinitrobenzene (TATB) and yttria‐stabilized zirconia (YSZ), an SEM certified standard. Mie theory was used to reduce the LLS data. The spherical nature of the YSZ made it a good candidate for LLS. Variations in n , the refractive index, and iκ, the imaginary component, produced very little change in the PSD. However, changing the carrier liquid from H 2 O to a 40% aqueous sucrose solution, thereby changing the carrier refractive index, n 0 , substantially affected the PSD. The Mie complex refractive indices for the YSZ were n = 2.200, iκ = 0.100, with a 40% aqueous sucrose solution, n 0 = 1.400. The triclinic crystal structure of TATB made refractive index determinations more difficult, so a study was conducted varying Mie parameters and comparing them to the same data reduced using the Fraunhofer theory. Changing the n and κ parameters produced PSD with a small concentration of particles less than 1 µm in size or none in this range. SEM images, Feret data, manual counting, and Fraunhofer data reduction indicate particles less than 1 µm are probably < 5% in concentration. The final selection of Mie parameters for TATB was n = 2.283, iκ = 0.1, and suspension medium, n 0 = 1.330. Finally, computations, using density functional theory produced similar parameters.

Feret diameter↗
DOE OSTI2021

Quantifying the effect of hydride microstructure on zirconium alloys embrittlement using image analysis

Since hydride microstructure can significantly influence Zr alloy nuclear fuel cladding’s ductility, a new metric has been developed to quantify hydride microstructure in 2D micrographs and relate it to crack propagation. As cladding failure usually results from a hoop stress, this new metric, called the Radial Hydride Continuous Path (RHCP), is based on quantifying the continuity of brittle hydride particles along the radial direction of the cladding tube. Compared to previous metrics, this approach more closely relates to the propensity of a crack to propagate radially through the cladding tube thickness. The RHCP takes into account hydride length, orientation, and connectivity to choose the optimal path for crack propagation through the cladding thickness. The RHCP can therefore be more closely linked to hydride embrittlement of the Zr alloy material, thus creating a relationship between material structure, properties, and performance. The new definition, along with previously proposed metrics such as the Radial Hydride Fraction (RHF), the Hydride Continuity Coefficient (HCC), and the Radial Hydride Continuity Factor (RHCF), have been implemented and automated in MATLAB. These codes are made available with this publication as supplementary materials. These metrics were verified by comparing their predictions of hydride morphology against expected values in simple cases, and the implementation of the new metric was validated by comparing its predictions with manual measurements of hydride microstructure performed on ImageJ. The RHCP was also validated against experimental measurements of fracture behavior and it was shown to correlate with cladding failure better than previous metrics. The information provided by these metrics will help accurately assess cladding integrity during operation, transportation, and storage.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Sintering effects on NpO 2 grain size and morphology: The role of precursor Np phase

Neptunium dioxide (NpO 2 ) is a key phase in nuclear material processing as a target material for the production of plutonium-238 ( 238 Pu) and has been historically synthesized via the calcination of a Np oxalate precursor. Alternative synthesis methods for NpO 2 are now more prevalent, necessitating their study and comparison with the more common oxalate route. The purpose of this work was to investigate the microstructural properties of NpO 2 synthesized from a nitrate-based Np precursor phase via the assessment of NpO 2 particle size and morphology as a function of calcination temperature and time. Scanning electron microscopy (SEM) was used to probe the primary grain size and morphology of NpO 2 after calcination at temperatures ranging from 700 to 1100 °C and hold times ranging from 1 to 10 h. Post-image analysis using ImageJ software enabled the quantification of mean particle diameter. This analysis indicated that particle diameter increases with both increasing calcination temperature and hold time. Primary particles were shown to be clumped in irregular patterns into the overall rough, blocky aggregates, but this macroscopic morphology was not affected by calcination time or temperature. Although trends in primary grain size of NpO 2 were consistent with available literature from other Np precursor phases, the macroscopic morphology of the NpO 2 aggregates was quite different than reported for other precursors. Through comparison with historical literature on Np oxalate, this work emphasizes the importance of Np precursor on the physical properties of NpO 2 .

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2020

How “hot” are hotspots: Statistically localizing the high-activity areas on soil and rhizosphere images

The topic of microbial hotspots in soil requires not only visualizing their spatial distribution and biochemical analyses, but also statistical approaches to identify these hotspots and separate them from the surrounding activities (background). We hypothesized that each hotspot type (e.g. enzyme activities in the rhizosphere, root exudation, localization of herbicide accumulation) is a result of local process driven by biotic and/or abiotic factors, and the process rates in the hotspots are much faster than those in the soil background. We further hypothesized that the background and hotspot activities in soil belong to different statistical distributions. Consequently, hotspot determination should be based on statistical separation of activities significantly higher than the background. We analyzed for the statistical distributions of grey values on three groups of published images: 1) 14 C images of carbon input by roots into the rhizosphere, 2) 14 C glyphosate accumulation in the plant, and 3) zymogram of leucine aminopeptidase activity in rooted soil. The two Gaussian distributions were fit (the first representing the background, the second the hotspots) to the distribution of grey values in the images, the parameters (means and standard deviations, SD) of the fitted distributions were calculated, and the background was removed. Thus, we identified hotspots as areas outside of the Mean+2SD image intensity (corresponding to the upper ~ 2.5% of activity, being over 97.5% of background values) and finally, visualized images of solely hotspot locations. Finally, these results were compared with previously used decisions on hotspot intensity thresholding (i.e. Top-25% and 17 standard thresholding approaches in ImageJ) and discussed the advantages of the Mean+2SD as well as Mean+3SD approaches. These advantages include: i) simple unification of the thresholding approach for several imaging methods with various principles of activity distribution, ii) identification of hotspots with various activity levels, iii) analysis of “time-specific” hotspots in temporal sequences of images. Compared with 17 standard thresholding methods, we concluded that objectively elucidating and separating the hotspots should be based on statistical distribution analysis, e.g. using the Mean+2SD or Mean+3SD approaches. Furthermore, this simple Mean+2SD approach delivered suitable results for three groups of images and so, helps to understand the processes responsible for the highest activities and elucidate hotspots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay

Abstract Motivation The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. Results We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. Availability and implementation All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. Supplementary information Supplementary data are available at Bioinformatics online.

Hagemeijer, Marne C.↗
DOE OSTI2022

TXM-Sandbox : an open-source software for transmission X-ray microscopy data analysis

A transmission X-ray microscope (TXM) can investigate morphological and chemical information of a tens to hundred micrometre-thick specimen on a length scale of tens to hundreds of nanometres. It has broad applications in material sciences and battery research. TXM data processing is composed of multiple steps. A workflow software has been developed that integrates all the tools required for general TXM data processing and visualization. The software is written in Python and has a graphic user interface in Jupyter Notebook . Users have access to the intermediate analysis results within Jupyter Notebook and have options to insert extra data processing steps in addition to those that are integrated in the software. The software seamlessly integrates ImageJ as its primary image viewer, providing rich image visualization and processing routines. As a guide for users, several TXM specific data analysis issues and examples are also presented.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Real-time streaming tomographic reconstruction with on-demand data capturing and 3D zooming to regions of interest

Complex dynamic tomographic experiments at brilliant X-ray light sources require real-time feedback on the sample changes with respect to environmental conditions, selecting representative regions of interest for high-resolution scanning, and on-demand data saving mechanisms for storing only relevant projections acquired by fast area detectors and reducing data volumes. Here the implementation details of a 3D real-time imaging monitoring instrument, with zooming to a volume of interest with easy-to-use visualization via ImageJ , a tool familiar to most beamline users, is presented. The instrument relies on optimized data flow between the detector and processing machines and is implemented on commodity computers. The instrument has been developed at beamline 2-BM of the Advanced Photon Source, where the automatic lens changing mechanism for zooming is implemented with an Optique Peter microscope. Performance tests demonstrate the ability to process more than 3 GB of projection data per second and generate real-time 3D zooming with different magnification. These new capabilities are essential for new APS Upgrade instruments such as the projection microscope under development at beamline 32-ID. The efficacy of the proposed instrument was demonstrated during an in situ tomographic experiment on ice and gas hydrate formation in porous samples.

3D zooming↗
DOE OSTI2021

Color Change During Thermal Degradation of Polyolefin Electric Cable Insulations

Color change of electric cable insulations used in nuclear power plants (NPPs) is a non-destructive, quick and inexpensive technique to measure degradation. Quantification of color change is facilitated by a light booth of CIE D65 illuminant, a commercial camera and open-source software ImageJ with micaToolbox plugin. Yellowness index (YI) and total color difference (?E) are calculated from calibrated photos of a white cross-linked polyethylene (XLPE) and a black ethylene-propylene rubber (EPR) based specimens aged at 110°C, 121°C, 136°C and 150°C after 1~640 days. Using the same setup and software, pixelwise ?E profile is determined for the cross-sectional photo of a white EPR specimen, where heterogeneous aging is detected.

cable aging, color analysis↗