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At least 37 records · Page 2

XRFtomo

Based on [1], XRFtomo brings together a variety of image processing tools used for preparing, processing and reconstructing 3D renditions of samples imaged using a synchrotron-based x-ray fluorescence (XRF) microprobe or nanoprobe at the Advanced Photon Source (APS). This software bridges the gap between data acquisition and visualization by providing tools to adjust for misalignment in the imaging process and tools for running reconstructions[2], all with the use of a GUI or command line. XRFtomo accepts .h5 files processed through MAPS[3] and it outputs reconstructed cross-sections, projections, sinograms, metadata, and a configuration file with last-used parameters for rapid processing the next time the program is launched. These images serve as inputs for other 3D visualization software for generating volumetric renderings and animations.

Marin, Fabrico↗

Development of a lab-scale, high-resolution, tube-generated X-ray computed-tomography system for three-dimensional (3D) materials characterization

The design and construction of a modular high resolution X-ray computed tomography (XCT) system is highlighted in this paper. The design approach is detailed for meeting a specified set of instrument performance goals tailored towards experimental versatility and high resolution imaging. The XCT tool is unique in the detector and X-ray source design configuration, enabling control in the balance between detection efficiency and spatial resolution. The system package is also unique: The sample manipulation approach implemented enables a wide gamut of in situ experimentation to analyze structure evolution under applied stimulus, by optimizing scan conditions through a high degree of controllability. The component selection and design process is detailed: Incorporated components are specified, custom designs are shared, and the approach for their integration into a fully functional XCT scanner is provided. Custom designs discussed include the dual-target X-ray source cradle which maintains position and trajectory of the beam between the two X-ray target configurations with respect to a scintillator mounting and positioning assembly and the imaging sensor, as well as a novel large-format X-ray detector with enhanced adaptability. The instrument is discussed from an operational point of view, including the details of data acquisition and processing implemented for 3D imaging via micro-CT. The performance of the instrument is demonstrated on a silica-glass particle/hydroxyl-terminated-polybutadiene (HTPB) matrix binder PBX simulant. Post-scan data processing, specifically segmentation of the sample's relevant microstructure from the 3D reconstruction, is provided to demonstrate the utility of the instrument. - Highlights: • Custom built X-ray tomography system for microstructural characterization • Detector design for maximizing polychromatic X-ray detection efficiency • X-ray design offered for maximizing X-ray flux with respect to imaging resolution • Novel lab-scale XCT data acquisition and data processing methods • 3D characterization of glass-bead mock plastic-bonded-explosive stimulant.

36 MATERIALS SCIENCE↗

Snapshot 3D tracking of insulin granules in live cells

Rapid and accurate volumetric imaging remains a challenge, yet has the potential to enhance understanding of cell function. We developed and used a multifocal microscope (MFM) for 3D snapshot imaging to allow 3D tracking of insulin granules labeled with mCherry in MIN6 cells. MFM employs a special diffractive optical element (DOE) to simultaneously image multiple focal planes. This simultaneous acquisition of information deteunines the 3D location of single objects at a speed only limited by the array detector's frame rate. We validated the accuracy of MFM imaging/tracking with fluorescence beads; the 3D positions and trajectories of single fluorescence beads can be detelinined accurately over a wide range of spatial and temporal scales. The 3D positions and trajectories of single insulin granules in a 3.2um deep volume were deteunined with imaging processing that combines 3D decovolution, shift correction, and finally tracking using the Imaris software package. We find that the motion of the granules is super diffusive, but less so in 3D than 2D for cells grown on coverslip surfaces, suggesting an anisotropy in the cytoskeleton (e.g. microtubules and action).

3D tracking↗

Progress Update on Iterative Reconstruction of Neutron Tomographic Images

This report satisfies the fiscal year 2016 technical deliverable to report on progress in development of fast iterative reconstruction algorithms for project OR16-3DTomography-PD2Jb, "3D Tomography and Image Processing Using Fast Neutrons." This project has two overall goals. The first of these goals is to extend associated-particle fast neutron transmission and, particularly, induced-reaction tomographic imaging algorithms to three dimensions. The second of these goals is to automatically segment the resultant tomographic images into constituent parts, and then extract information about the parts, such as the class of shape and potentially shape parameters. This report addresses of the component of the project concerned with three-dimensional (3D) image reconstruction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Fractal breakage of porous carbonate sand particles: Microstructures and mechanisms

In situ, three-dimensional (3D) characterizations of particle breakage in porous carbonate sands are presented, for the first time, with synchrotron-based micro computed tomography. Evolution of grain-scale characteristics are identified and quantified via elaborate image processing and topology analyses. The sequential 3D images reveal distinctly different fracture mechanisms for carbonate sands from silica sands. The angular shape of carbonate sand particles facilitates bending fracture, and particles with a lower sphericity and a higher porosity are more prone to break. 3D crack networks extracted from fractured particles imply considerable cleavage along initial pores. The fractal dimension of crack networks increases with external loading due to crack branching via cleavage. The resultant fragment size distribution also appears fractal and the fractal feature is valid down to the breakage limit of calcium carbonate. Crack propagation along the initial pores reduces the energy barrier for particle breakage and thus fracture strength of particles

Carbonate sands↗

Using superconducting undulator for enhanced imaging capabilities of MaRIE

MaRIE x-ray free electron laser (FEL) is envisioned to deliver a burst of closely spaced in time pulses for enabling the capability of studying the dynamic processes in a sample. MaRIE capability can be largely enhanced using the superconducting undulator, which has the capability of doubling its period. This technology will allow reaching the photon energy as low as ~200-500 eV. As a result, the MaRIE facility will have a broader photon energy range enabling a larger variety of experiments. The soft x-ray capability is more likely to achieve the 3D imaging of dynamic processes in noncrystal materials than the hard x-ray capability alone.

42 ENGINEERING↗

Sandia MEMS Visualization Tools v. 3.0

This is a revision to the Sandia MEMS Visualization Tools. It replaces all previous versions. New features in this version: Support for AutoCAD 2014 and 2015 . This CD contains an integrated set of electronic files that: a) Provides a 2D Process Visualizer that generates cross-section images of devices constructed using the SUMMiT V fabrication process. b) Provides a 3D Visualizer that generates 3D images of devices constructed using the SUMMiT V fabrication process. c) Provides a MEMS 3D Model generator that creates 3D solid models of devices constructed using the SUMMiT V fabrication process. While there exists some files on the CD that are used in conjunction with software package AutoCAD , these files are not intended for use independent of the CD. Note that the customer must purchase his/her own copy of AutoCAD to use with these files.

Yarberry, Victor↗

TH-AB-209-04: 3D Light Sheet Luminescence Imaging with Cherenkov Radiation

Purpose: To recover a three-dimensional density distribution of luminescent molecular probes located several centimeters deep within a highly scattering tissue. Methods: We developed a novel sheet beam Cherenkov-excited luminescence scanned imaging (CELSI) methodology. The sample was irradiated by a horizontally oriented, vertically scanned 6 MV X-ray sheet beam (200mm × 5mm, 0.2mm vertical step) from a radiotherapy linear accelerator. The resulting Cherenkov light emission – and thus luminescent probe excitation – occurred exclusively along the irradiation plane due to a short diffusion path of secondary particles and Cherenkov photons. Cherenkov-excited luminescence was detected orthogonally to the sheet beam by gated, intensified charge coupled device camera. Analogously to light sheet microscopy, a series of luminescence images was taken for varied axial positions (depths) of the Cherenkov light sheet in sample. Knowledge of the excitation plane position allowed a 3D image stack deconvolution and depth-variant attenuation correction. The 3D image post-processing yielded a true spatial density distribution of luminescent molecules in highly scattering tissue. Results: We recovered a three-dimensional shape and position of 400 µL lesion-mimicking phantom tubes containing 25 µM solution of PtG4 molecular probe from 3 centimeter deep tissue-like media. The high sensitivity of CELSI also allowed resolving 100 micron capillaries of test solution. Functional information of partial oxygen pressure at the site of PtG4 molecular probe was recovered from luminescence lifetime CELSI. Finally, in-vivo sheet beam CELSI localized milimeter-sized PtG4-labelled tumor phantoms in multiple biological objects (hairless mice) from single scan. Conclusion: Presented sheet beam CELSI technique greatly extended the useful depth range of luminescence molecular imaging. More importantly, the light sheet microscopy approach was successfully adapted to CELSI, providing means to recover a completely attenuation-corrected 3D image of luminescent probe distribution. Gated CELSI acquisition yielded functional information of a spatially resolved oxygen concentration map of deep lying targets. This work was supported by NIH research grant R01CA109558 and R21EB017559, as well as by Pilot Grant Funds from the Norris Cotton Cancer Center.

60 APPLIED LIFE SCIENCES↗

SU-F-R-20: Image Texture Features Correlate with Time to Local Failure in Lung SBRT Patients

Purpose: To explore possible correlation between CT image-based texture and histogram features and time-to-local-failure in early stage non-small cell lung cancer (NSCLC) patients treated with stereotactic body radiotherapy (SBRT).Methods and Materials: From an IRB-approved lung SBRT registry for patients treated between 2009–2013 we selected 48 (20 male, 28 female) patients with local failure. Median patient age was 72.3±10.3 years. Mean time to local failure was 15 ± 7.1 months. Physician-contoured gross tumor volumes (GTV) on the planning CT images were processed and 3D gray-level co-occurrence matrix (GLCM) based texture and histogram features were calculated in Matlab. Data were exported to R and a multiple linear regression model was used to examine the relationship between texture features and time-to-local-failure. Results: Multiple linear regression revealed that entropy (p=0.0233, multiple R2=0.60) from GLCM-based texture analysis and the standard deviation (p=0.0194, multiple R2=0.60) from the histogram-based features were statistically significantly correlated with the time-to-local-failure. Conclusion: Image-based texture analysis can be used to predict certain aspects of treatment outcomes of NSCLC patients treated with SBRT. We found entropy and standard deviation calculated for the GTV on the CT images displayed a statistically significant correlation with and time-to-local-failure in lung SBRT patients.

60 APPLIED LIFE SCIENCES↗

Progress Update on Iterative Reconstruction of Neutron Tomographic Images, 2019

The fiscal year (FY) 2019 update of this report satisfies the technical deliverable “Simultaneous reconstruction of simultaneous observables” for project OR16-ML-3DTomography-PD3Jb, “3D Tomography and Image Processing Using Fast Neutrons.” At its inception, this project had two overall goals. The first of these goals was to extend associated-particle fast neutron transmission and, particularly, induced-reaction tomographic imaging algorithms to three dimensions. The second of these goals was to automatically segment the resultant tomographic images into constituent parts and then extract information about the parts, such as the class of shape and potentially shape parameters. This report addresses the component of the project concerned with three-dimensional (3D) image reconstruction and represents the cumulative progress to date. In particular, it addresses the ability to decompose neutrons arriving at times consistent with transmission into transmission and small-angle scattering. Because incremental progress in each year builds on the previous year’s progress and end-ofyear status, progress is most usefully recorded in a cumulative document where incremental progress is reported on a year-by-year basis. Consequently, this report constitutes an update of the last 3 years’ reports [1, 2, 14]. The present year’s progress is detailed in Section 7.

47 OTHER INSTRUMENTATION↗

Oak Ridge National Laboratory Progress Update on Segmentation of Neutron Tomographic Images, 2017

The present report documents progress regarding segmentation of fast-neutron tomographic images of objects consisting of assemblies of machined parts with distinct boundaries. This report satisfies the fiscal year 2017 technical deliverable for project OR16-3DTomography-PD3Jb, “3D Tomography and Image Processing Using Fast Neutrons,” to report on the extension of geometric shape-finding algorithms to three dimensions. The project has two overall goals. The first of these goals is to extend associated particle fast neutron transmission and, particularly, induced-reaction tomographic imaging algorithms to three dimensions. The second of these goals is to automatically segment the resultant tomographic images into constituent parts, and then extract information about the parts, such as the class of shape and potentially the shape parameters. This report addresses continued progress in the component of the project concerned with image segmentation.

3D tomography↗

Progress Update on Segmentation of Neutron Tomographic Images, 2018

The present report documents the techniques developed to segment fast-neutron tomographic images of objects consisting of assemblies of machined parts with distinct boundaries. This report satisfies the fiscal year 2018 technical deliverable for project OR16-3DTomography-PD3Jb, “3D Tomography and Image Processing Using Fast Neutrons,” to report on the extension of geometric shape-finding algorithms to three dimensions. The project has two overall goals. The first of these goals is to extend associated-particle fast-neutron transmission and, particularly, induced-reaction tomographic imaging algorithms to three dimensions. This aspect of the project is beyond the scope of this report. The second goal is to automatically segment the resultant tomographic images into constituent parts and then extract information about the parts, such as the class of shape and potentially the shape parameters. This report describes progress for the image segmentation part of the project. Imaging techniques have been developed as high-confidence methods for confirming the presence and configuration of special nuclear materials (SNM). This high confidence is achieved at the cost of revealing considerable information that may be undesirable to share with the operator of the equipment. One potential way to make use of the high-confidence of imaging methods without revealing imaging data is to employ automated analysis that can extract meaningful attributes of the SNM without showing imaging data to the operator. An essential step of this automated analysis is the segmentation of the image into its constituent parts. For example, a three-dimensional (3D) fast-neutron tomographic image of an assembly containing uranium could be reconstructed and then segmented into discrete parts. The properties of a constituent part identified as uranium would be of interest and could be extracted. For instance, the volume and density of the part would together determine its mass. Moreover, its shape might be expected to fall into a particular geometric class, such as a cube, cylinder, or sphere, and the parameters of the shape (such as side length, height, or diameter) would be expected to fall in a given range. In such an analysis, automated identification of the boundaries and properties of the uranium part is an essential step. A key goal of the present work is to infer the boundaries of objects in fast-neutron tomographic images via the general method of image segmentation. Development of this capability can be broken into more manageable steps, including 1. operator-guided segmentation of two-dimensional (2D) fast-neutron tomographic images, 2. operator-guided segmentation of 3D fast-neutron tomographic images, 3. development of automated segmentation algorithms, and 4. extraction of shape parameters from constituent volumes in 3D. In the first year, the project team reported progress on the first step. Last year, progress on the second step, the extension into 3D, was reported with application to simulated data. The present report describes additional progress on the second step, and progress toward the third step, automated segmentation algorithms. In particular, a multiphase level set approach for image segmentation in three dimensions has been applied to measured 3D data for the first time. Activities related to the fourth step will also be reported, but it will focus on estimation of 3D volumes rather than shape parameters. In this report, the steps before image segmentation will be described, and the multiphase level sets approach to image segmentation will be briefly reviewed. This will be followed by a discussion of the issues encountered when applying the level set technique to measured 3D transmission images, and then a description of the inclusion of induced-reaction data will be provided. Finally, segmentation results for various measured target assemblies will be presented and the image segmentation portion of this project will be summarized and future directions will be discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

3D characterization of trans- and inter-lamellar fatigue crack in (α + β) Ti alloy

This paper presents a three dimensional image processing strategy that has been developed to quantitatively analyze and correlate the path of a fatigue crack with the lamellar microstructure found in Ti-6246. The analysis is carried out on X-ray microtomography images acquired in situ during uniaxial fatigue testing. The crack, the primary β-grain boundaries and the α lamellae have been segmented separately and merged for the first time to allow a better characterization and understanding of their mutual interaction. This has particularly emphasized the role of translamellar crack growth at a very high propagation angle with regard to the lamellar orientation, supporting the central role of colonies favorably oriented for basal 〈a〉 slip to guide the crack in the fully lamellar microstructure of Ti alloy. - Highlights: • 3D tomography images reveal strong short fatigue crack interaction with α lamellae. • Proposed 3D image processing methodology makes their segmentation possible. • Crack-lamellae orientation maps show prevalence of translamellar cracking. • Angle study comforts the influence of basal/prismatic slip on crack path.

36 MATERIALS SCIENCE↗

LUNUS, Version 0.1a

LUNUS software for generating 3D maps of diffuse scattering from macromolecular X-ray crystallography diffraction images. A set of tools needed for advanced refinement of crystal structures and crystallographic charge density models. Includes tools for processing X--ray diffraction images, charge density maps, and structure factors for analysis of diffuse X-ray scattering and charge density variations in crystallography. Specific methods include: elementary algebraic operations on images and 3D lattices; fourier transform of images and 3D lattices; image processing to measure diffuse intensity; crystallographic refinement; and 3D integration of diffuse intensity.

Wall, Michael↗

LUNUS, Version 0.1a

LUNUS software for generating 3D maps of diffuse scattering from macromolecular X-ray crystallography diffraction images. A set of tools needed for advanced refinement of crystal structures and crystallographic charge density models. Includes tools for processing X--ray diffraction images, charge density maps, and structure factors for analysis of diffuse X-ray scattering and charge density variations in crystallography. Specific methods include: elementary algebraic operations on images and 3D lattices; fourier transform of images and 3D lattices; image processing to measure diffuse intensity; crystallographic refinement; and 3D integration of diffuse intensity.

Wall, Michael↗

Nanoscale Resolution 3D Snapshot Particle Tracking by Multifocal Microscopy

Accurate, precise, and rapid particle tracking in three dimensions remains a challenge; yet, its achievement will significantly enhance our understanding of living systems. We developed a multifocal microscopy (MFM) that allows snapshot acquisition of the imaging data, and an associated image processing approach, that together allow simultaneous 3D tracking of many fluorescent particles with nanoscale resolution. The 3D tracking was validated by measuring a known trajectory of a fluorescent bead with an axial accuracy of 19 nm through an image depth (axial range) of 3 pm and 4 nm precision of axial localization through an image depth of 4 pm. A second test obtained a uniform axial probability distribution and Brownian dynamics of beads diffusing in solution. We also validated the MFM approach by imaging fluorescent beads immobilized in gels and comparing the 3D localizations to their "ground truth" positions obtained from a confocal microscopy z-stack of finely spaced images. Finally, we applied our MFM and image processing approach to obtain 3D trajectories of insulin granules in pseudoislets of MIN6 cells to demonstrate its compatibility with complex biological systems. Our study demonstrates that multifocal microscopy allows rapid (video rate) and simultaneous 3D tracking of many "particles" with nanoscale accuracy and precision in a wide range of systems, including over spatial scales relevant to whole live cells.

3D Tracking↗

Quantitative microstructural investigation of 3D-printed and cast cement pastes using micro-computed tomography and image analysis

Highlights: • Processing alters the microstructure in 3D-printed lamellar cubic element. • A unique patterned and connected pore microstructure network exists. • Micro-channels are connected through micro-pores present at interfaces regions. • Three distinct pore volume domains exists in hardened microstructure. • Volume and frequency of pore, hydrated, and unhydrated clusters are dissimilar. Microstructural phases and mechanical properties of lamellar 3D-printed and cast hardened cement paste (hcp) elements were investigated using a lab-based X-ray microscope at two levels of magnification (0.4× and 4×). K-means clustering was used for quantitative image analysis. The entire volume of intact 3-days-old 3D-printed and cast hcp elements was characterized at 0.4× magnification. Three microstructural features (macro-pores, micro-channels, and interfacial micro-pores) were found to reside in three distinct pore size domains. The largest pores of the 3D-printed element were larger than the largest pores of the reference cast hcp element. Moreover, the smallest pore sizes of the 3D-printed element were found to be smaller than those present in the cast counterparts. Micro-channels were found to be connected to one another through the micro-pores present at interfacial regions, indicating the presence of a uniquely patterned and interconnected pore network. The role of locally weak and porous interfaces on mechanical response and fracture properties is discussed.

36 MATERIALS SCIENCE↗

Macro-carriers of plastic deformation of steel surface layers detected by digital image correlation

This paper presents a study of characteristics of an evolution of deformation fields in surface layers of medium-carbon low-alloy specimens under compression. The experiments were performed on the “Universal Testing Machine 4500” using a digital stereoscopic image processing system Vic-3D. A transition between stages is reflected as deformation redistribution on the near-surface layers. Electronic microscopy shows that the structure of the steel is a mixture of pearlite and ferrite grains. A proportion of pearlite is 40% and ferrite is 60%.

36 MATERIALS SCIENCE↗