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DOE OSTI2020

Windowed Fourier transform and cross-correlation algorithms for molecular tagging velocimetry

In this study, simulated and experimental molecular tagging velocimetry (MTV) images have been analyzed with a technique commonly used to process grid images on surfaces, the windowed Fourier transform with local spectrum analysis (WFT-LSA). A systematic synthetic image study of the modulation transfer function (MTF) and error tendencies of the WFT-LSA was performed and compared with a PIV-style cross-correlation algorithm to see if advanced strategies such as iterative image deformation can improve analysis of gridded images with high noise levels. Testing of single-pass algorithms showed that in typical MTV images, the WFT-LSA yields significantly lower bias errors than cross-correlation (CC) at displacements greater than 1 pixel but slightly higher random error at all displacements and image conditions. Analysis of the MTF shows that CC provided better resolution of spatial fluctuations than the WFT-LSA in many combinations of grid size and interrogation window. Tests of image deformation algorithms showed that the gap in performance between CC and WFT-LSA is maintained even as both methods improve. Additionally, WFT-LSA and CC methods are applied to real MTV experiments in high-speed gas jet flows. A preliminary analysis of phosphorescence lifetime provided by acetone vapor excited at 266 nm is used for assessing the required gas speeds for making MTV application feasible. The application of WFT-LSA to real MTV images demonstrates the ability of the algorithm to handle further real-world effects that could not be considered in the synthetic image analysis, like reduced signal-to-noise ratio and non-uniform intensity of the tagging grid across the image introduced by the actual laser beam energy distribution. With experimental images, CC is more accurate with shear flows but less robust to high noise levels than WFT-LSA, as predicted by the synthetic image analysis.

42 ENGINEERING↗

DOE OSTI2012

Comparative analysis of nonlinear dimensionality reduction techniques for breast MRI segmentation

Purpose: Visualization of anatomical structures using radiological imaging methods is an important tool in medicine to differentiate normal from pathological tissue and can generate large amounts of data for a radiologist to read. Integrating these large data sets is difficult and time-consuming. A new approach uses both supervised and unsupervised advanced machine learning techniques to visualize and segment radiological data. This study describes the application of a novel hybrid scheme, based on combining wavelet transform and nonlinear dimensionality reduction (NLDR) methods, to breast magnetic resonance imaging (MRI) data using three well-established NLDR techniques, namely, ISOMAP, local linear embedding (LLE), and diffusion maps (DfM), to perform a comparative performance analysis. Methods: Twenty-five breast lesion subjects were scanned using a 3T scanner. MRI sequences used were T1-weighted, T2-weighted, diffusion-weighted imaging (DWI), and dynamic contrast-enhanced (DCE) imaging. The hybrid scheme consisted of two steps: preprocessing and postprocessing of the data. The preprocessing step was applied for B{sub 1} inhomogeneity correction, image registration, and wavelet-based image compression to match and denoise the data. In the postprocessing step, MRI parameters were considered data dimensions and the NLDR-based hybrid approach was applied to integrate the MRI parameters into a single image, termed the embedded image. This was achieved by mapping all pixel intensities from the higher dimension to a lower dimensional (embedded) space. For validation, the authors compared the hybrid NLDR with linear methods of principal component analysis (PCA) and multidimensional scaling (MDS) using synthetic data. For the clinical application, the authors used breast MRI data, comparison was performed using the postcontrast DCE MRI image and evaluating the congruence of the segmented lesions. Results: The NLDR-based hybrid approach was able to define and segment both synthetic and clinical data. In the synthetic data, the authors demonstrated the performance of the NLDR method compared with conventional linear DR methods. The NLDR approach enabled successful segmentation of the structures, whereas, in most cases, PCA and MDS failed. The NLDR approach was able to segment different breast tissue types with a high accuracy and the embedded image of the breast MRI data demonstrated fuzzy boundaries between the different types of breast tissue, i.e., fatty, glandular, and tissue with lesions (>86%). Conclusions: The proposed hybrid NLDR methods were able to segment clinical breast data with a high accuracy and construct an embedded image that visualized the contribution of different radiological parameters.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2014

Prostatome: A combined anatomical and disease based MRI atlas of the prostate

Purpose: In this work, the authors introduce a novel framework, the anatomically constrained registration (AnCoR) scheme and apply it to create a fused anatomic-disease atlas of the prostate which the authors refer to as the prostatome. The prostatome combines a MRI based anatomic and a histology based disease atlas. Statistical imaging atlases allow for the integration of information across multiple scales and imaging modalities into a single canonical representation, in turn enabling a fused anatomical-disease representation which may facilitate the characterization of disease appearance relative to anatomic structures. While statistical atlases have been extensively developed and studied for the brain, approaches that have attempted to combine pathology and imaging data for study of prostate pathology are not extant. This works seeks to address this gap. Methods: The AnCoR framework optimizes a scoring function composed of two surface (prostate and central gland) misalignment measures and one intensity-based similarity term. This ensures the correct mapping of anatomic regions into the atlas, even when regional MRI intensities are inconsistent or highly variable between subjects. The framework allows for creation of an anatomic imaging and a disease atlas, while enabling their fusion into the anatomic imaging-disease atlas. The atlas presented here was constructed using 83 subjects with biopsy confirmed cancer who had pre-operative MRI (collected at two institutions) followed by radical prostatectomy. The imaging atlas results from mapping thein vivo MRI into the canonical space, while the anatomic regions serve as domain constraints. Elastic co-registration MRI and corresponding ex vivo histology provides “ground truth” mapping of cancer extent on in vivo imaging for 23 subjects. Results: AnCoR was evaluated relative to alternative construction strategies that use either MRI intensities or the prostate surface alone for registration. The AnCoR framework yielded a central gland Dice similarity coefficient (DSC) of 90%, and prostate DSC of 88%, while the misalignment of the urethra and verumontanum was found to be 3.45 mm, and 4.73 mm, respectively, which were measured to be significantly smaller compared to the alternative strategies. As might have been anticipated from our limited cohort of biopsy confirmed cancers, the disease atlas showed that most of the tumor extent was limited to the peripheral zone. Moreover, central gland tumors were typically larger in size, possibly because they are only discernible at a much later stage. Conclusions: The authors presented the AnCoR framework to explicitly model anatomic constraints for the construction of a fused anatomic imaging-disease atlas. The framework was applied to constructing a preliminary version of an anatomic-disease atlas of the prostate, the prostatome. The prostatome could facilitate the quantitative characterization of gland morphology and imaging features of prostate cancer. These techniques, may be applied on a large sample size data set to create a fully developed prostatome that could serve as a spatial prior for targeted biopsies by urologists. Additionally, the AnCoR framework could allow for incorporation of complementary imaging and molecular data, thereby enabling their careful correlation for population based radio-omics studies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

SU-E-J-204: Can a Commercial System for MR-IGRT Be Used to Treat Patients Without Acquiring a CT Scan?

Patients treated using a magnetic-resonance image guided radiation therapy (MR-IGRT) system received both CT and MR simulations. During planning, the CT is used to determine relative electron density (RED) using a calibration table. This study aims to investigate the feasibility of MR-only treatments by comparing CT-computed dose distributions to those computed with combinations of water (1.0), lung (0.26), tissue (1.02), and bone (1.12) bulk RED overrides, and to identify the effects of the magnetic field on the RED-overridden doses. Methods: Four patients who received treatment using a commercial MR-IGRT system were analyzed (1 lung, 2 abdomen, and 1 pelvis). The clinical plans were computed using the first fraction MRI as primary, and the simulation CT as secondary for REDs. Plans were reoptimized using default bulk RED overrides (water/lung and tissue/lung for the lung patient, water/bone, tissue/bone, water only, and tissue only for the abdomen and pelvis patients). Additionally, each plan was re-optimized to include the static magnetic field. All plans were normalized to the same PTV coverage as the clinical plan. Dose-difference volumes and DVHs were computed for bulk density override plans, and 3D gamma analyses between each plan and its accompanying magnetic field plan were performed using 3%/3 mm dose difference and distance-to-agreement criteria using the PTV and Skin as masking structures. Results: The average differences in PTV and organs-at-risk mean dose for all RED combinations tested were −0.19 Gy (−0.62 – 0.06 Gy) and −0.34 Gy (−1.76 – 0.33 Gy), respectively. The average PTV and Skin gamma pass rates for all RED combinations tested were 99.88% (99.5% – 100%) and 98. 35% (96.3% – 99.6%). No systematic differences in DVHs or isodoses were observed. Conclusions: It is likely that that a commercial MR-IGRT system may produce high quality treatment plans without the need for CT scans. Authors of this abstract are members of the Washington University Radiation Oncology department, which has a research agreement with ViewRay, Inc.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

A 1.5 T transverse magnetic field in radiotherapy of rectal cancer: Impact on the dose distribution

Purpose: MRI guidance during radiotherapy has the potential to enable more accurate dose delivery, optimizing the balance between local control and treatment related toxicity. However, the presence of a permanent magnetic field influences the dose delivery, especially around air cavities. Here, electrons are able to return to the surface through which they entered the air cavity (electron return effect, ERE) locally resulting in dose hot- and cold-spots. Where RT of rectal cancer patients might benefit from MRI guidance for margin reduction, air cavities in and around the target volume are frequently present. The purpose of this research is to evaluate the impact of the presence of a 1.5 T transverse magnetic field on dose delivery in patients with rectal cancer. Methods: Ten patients treated with 5 × 5 Gy RT having large changes in pelvic air content were selected out of a cohort of 33 patients. On the planning CT, a 1.5 T, 6 MV, 7-field intensity modulated radiotherapy (IMRT) plan was created. This plan was subsequently recalculated on daily CT scans. For each daily CT, the CTV V{sub 95%} and V{sub 107%} and bowel area V{sub 5Gy}, V{sub 10Gy}, V{sub 15Gy}, V{sub 20Gy}, and V{sub 25Gy} were calculated to evaluate the changes in dose distribution from fraction to fraction. For comparison, the authors repeated this procedure for the 0 T situation. To study the effect of changing air cavities separate from other anatomical changes, the authors also generated artificial air cavities in the CTV of one patient (2 and 5 cm diameter), in the high dose gradient region (2 cm), and in the low dose area (2 cm). Treatment plans were optimized without and with each simulated air cavity. For appearing and disappearing air cavities, the CTV V{sub 95%} and V{sub 107%} were evaluated. The authors also evaluated the ERE separate from attenuation changes locally around appearing gas pockets. Results: For the ten patients, at 1.5 T, the V{sub 95%} was influenced by both appearing and disappearing air, and dropped to <98% in 2 out of 50 fractions due a disappearing air cavity of 150 cm{sup 3}. V{sub 95%} differences between 0 and 1.5 T were all within 2%. The V{sub 107%} was below 1% in 46 out of 50 fractions, and increased to 3% in the remaining fractions due to appearing air of around 120 cm{sup 3}. For comparison, V{sub 107%} was <1% at 0 T for all fractions. In the bowel area, the V{sub 15Gy} varied strongest from fraction to fraction, but differences between 1.5 and 0 T were minimal with an average difference of 2.3 cm{sup 3} (SD = 18.7 cm{sup 3}, p = 0.38). For the simulated air cavities, the ERE resulted in cold-spots maximally 5% lower than prescribed and hot-spots maximally 6% higher than prescribed. Conclusions: The presence of a 1.5 T magnetic field has an impact on the dose distribution when the air content changes of within a few percent in these selected rectal cancer patients. The authors consider this influence of the transverse magnetic field on the dose distribution in IMRT for rectal cancer patients clinically acceptable.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2012

Portable MRI [Slides]

This project proposes to: (1) provide the power of MRI to situations where it presently isn't available; (2) perform the engineering required to move from lab to a functional prototype; and (3) leverage significant existing infrastructure and capability in ultra-low field MRI. The reasons for doing this: (1) MRI is the most powerful tool for imaging soft-tissue (e.g. brain); (2) Billions don't have access due to cost or safety issues; (3) metal will heat/move in high magnetic fields; (4) Millions of cases of traumatic brain injury in US alone; (5) even more of non-traumatic brain injury; (6) (e.g. stroke, infection, chemical exposure); (7) Need for early diagnostic; (8) 'Signature' wound of recent conflicts; (9) 22% of injuries; (10) Implications for post-traumatic stress disorder; and (11) chronic traumatic encephalopathy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2024

Atomic resolution scanning transmission electron microscopy at liquid helium temperatures for quantum materials

Fundamental quantum phenomena in condensed matter, ranging from correlated electron systems to quantum information processors, manifest their emergent characteristics and behaviors predominantly at low temperatures. This necessitates the use of liquid helium (LHe) cooling for experimental observation. Atomic resolution scanning transmission electron microscopy combined with LHe cooling (cryo-STEM) provides a powerful characterization technique to probe local atomic structural modulations and their coupling with charge, spin and orbital degrees-of-freedom in quantum materials. However, achieving atomic resolution in cryo-STEM is exceptionally challenging, primarily due to sample drifts arising from temperature changes and noises associated with LHe bubbling, turbulent gas flow, etc. In this work, we demonstrate atomic resolution cryo-STEM imaging at LHe temperatures using a commercial side-entry LHe cooling holder. Firstly, we examine STEM imaging performance as a function of He gas flow rate, identifying two primary noise sources: He-gas pulsing and He-gas bubbling. Secondly, we propose two strategies to achieve low noise conditions for atomic resolution STEM imaging: either by temporarily suppressing He gas flow rate using the needle valve or by acquiring images during the natural warming process. Lastly, we show the applications of image acquisition methods and image processing techniques in investigating structural phase transitions in Cr 2 Ge 2 Te 6 , CuIr 2 S 4 , and CrCl 3 . In conclusion, our findings represent an advance in the field of atomic resolution electron microscopy imaging for quantum materials and devices at LHe temperatures, which can be applied to other commercial side-entry LHe cooling TEM holders.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes

Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specifc contextual clues and requires no training. This approach generalizes across diferent modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal refectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fdelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufcient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

Ultrafast X-ray imaging of laser–metal additive manufacturing processes

The high-speed synchrotron X-ray imaging technique was synchronized with a custom-built laser-melting setup to capture the dynamics of laser powder-bed fusion processes in situ . Various significant phenomena, including vapor-depression and melt-pool dynamics and powder-spatter ejection, were captured with high spatial and temporal resolution. Imaging frame rates of up to 10 MHz were used to capture the rapid changes in these highly dynamic phenomena. At the same time, relatively slow frame rates were employed to capture large-scale changes during the process. This experimental platform will be vital in the further understanding of laser additive manufacturing processes and will be particularly helpful in guiding efforts to reduce or eliminate microstructural defects in additively manufactured parts.

laser powder bed fusion↗

DOE OSTI2012

Image features for misalignment correction in medical flat-detector CT

Purpose: Misalignment artifacts are a serious problem in medical flat-detector computed tomography. Generally, the geometrical parameters, which are essential for reconstruction, are provided by preceding calibration routines. These procedures are time consuming and the later use of stored parameters is sensitive toward external impacts or patient movement. The method of choice in a clinical environment would be a markerless online-calibration procedure that allows flexible scan trajectories and simultaneously corrects misalignment and motion artifacts during the reconstruction process. Therefore, different image features were evaluated according to their capability of quantifying misalignment. Methods: Projections of the FORBILD head and thorax phantoms were simulated. Additionally, acquisitions of a head phantom and patient data were used for evaluation. For the reconstruction different sources and magnitudes of misalignment were introduced in the geometry description. The resulting volumes were analyzed by entropy (based on the gray-level histogram), total variation, Gabor filter texture features, Haralick co-occurrence features, and Tamura texture features. The feature results were compared to the back-projection mismatch of the disturbed geometry. Results: The evaluations demonstrate the ability of several well-established image features to classify misalignment. The authors elaborated the particular suitability of the gray-level histogram-based entropy on identifying misalignment artifacts, after applying an appropriate window level (bone window). Conclusions: Some of the proposed feature extraction algorithms show a strong correlation with the misalignment level. Especially, entropy-based methods showed very good correspondence, with the best of these being the type that uses the gray-level histogram for calculation. This makes it a suitable image feature for online-calibration.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Vera C. Rubin Observatory Prompt Products

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

Vera C. Rubin Observatory Prompt Products: alert packets data

Data products produced by prompt and daily processing of images obtained in the Legacy Survey of Space and Time. These include realtime alerts sent to community alert brokers, newly-discovered Solar System Objects reported to the Minor Planet Center, processed visit and difference images, and source catalogs. Prompt Products are not a static single data release but continually grow throughout the ten-year LSST survey. This dataset is a subset of the full data release consisting of a dataset named alert packets. This dataset contains measurements for 5-sigma sources detected in difference images that were issued to the community brokers.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

A MultiDiscipline Approach to Digitizing Historic Seismograms

Retriever Technology has developed and has made available free of charge a seismogram digitization software package called SKATE (Seismogram Kit for Automatic Trace Extraction). We have developed an extensive set of algorithms that process seismogram image files, provide editing tools, and output time series data. The software is available online and free of charge at seismo.redfish.com. To demonstrate the speed and cost effectiveness of the software, we have processed over 30,000 images.

47 OTHER INSTRUMENTATION↗

DOE OSTI2016

SU-F-P-25: Dosimetric Changes of Brainstem Caused by Weight Loss During Intensity-Modulated Radiation Therapy for Nasopharyngeal Carcinoma

Purpose: To explore dosimetric effects of brainstem (BS) caused by weight loss during the course of intensity-modulated radiation therapy (IMRT) for nasopharyngeal carcinoma (NPC). Methods: Seventy-seven patients who were diagnosed with NPC by pathology biopsy have been enrolled. Every patients should receive weight measurement weekly and three times of computed tomography (CT) scans and replanning, at the 15th and 25th fraction during the treatment, respectively. The vertical diameter at the level of odontoid process (d1) and cervical vertebra 3 (d2) be measured from CT images (Supporting document Figure 1). All IMRT plans were designed by inverse planning with commercial treatment planning systems (Corvus 6.2 version, NOMOS Corporation). The dose differences between plan and actual delivery were generated to compare. Results: The weight loss was more in week 4–5 (3.21±2.19kg) than in week 1–3 (1.79±1.83kg) (Supporting document Figure 2). The d1 and d2 decreased was more significantly in week 4–5 than week 1–3, 2.83±1.75mm vs. 0.55±0.75mm and 2.98±2.96mm vs. 1.23±2.09mm, respectively. The maximum dose to the brainstem (BS Dmax) and the percentage of brainstem volume receiving ≥50Gy (BS V50) increased more significantly in week 4–5 than week 1–3, −3.02±5.49Gy vs. −1.85 ±4.88Gy and −1.85±4.88% vs. −0.77±3.32%, respectively. The changes of d1 and d2 and the BS-V50 and BS-Dmax were closely related to weight loss (p≤0.001)(Supporting document Table 1). Conclusion: The study results indicate that weight loss leads to the vertical diameter reduction, which results has a close relationship with dose of the brainstem during IMRT of NPC. This study was supported by Zhejiang Provincial Medicine and Health Foundation (2013KYB290) and Research Foundation of Science and Technology Department of Zhejiang Province 2015C33257.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Integrated and dynamic multi-spectroscopic in situ imaging of plant metabolism at the level of subcellular compartments. Final Report

The goals of this project was to develop integrated multi-spectral molecular imaging technologies (Raman, fluorescence, and mass spectrometry), that can assess, and image metabolic processes at the cellular and subcellular levels of plant organs. These imaging technologies were developed in the context of computational capabilities that integrated multi-spectral images with genome scale models of metabolism. The integrated molecular imaging technologies were developed in the biological context of autophagy that remodels membrane lipid topologies, which control spatially defined subcellular regions within plant cells and optimizes plant biomass productivity during environmental stresses that can limit biomass productivity.

09 BIOMASS FUELS↗

DOE OSTI2014

Apparatus and method for temperature mapping a turbine component in a high temperature combustion environment

Method and system for calibrating a thermal radiance map of a turbine component in a combustion environment. At least one spot (18) of material is disposed on a surface of the component. An infrared (IR) imager (14) is arranged so that the spot is within a field of view of the imager to acquire imaging data of the spot. A processor (30) is configured to process the imaging data to generate a sequence of images as a temperature of the combustion environment is increased. A monitor (42, 44) may be coupled to the processor to monitor the sequence of images of to determine an occurrence of a physical change of the spot as the temperature is increased. A calibration module (46) may be configured to assign a first temperature value to the surface of the turbine component when the occurrence of the physical change of the spot is determined.

47 OTHER INSTRUMENTATION↗

DOE OSTI2015

SU-E-J-15: Automatically Detect Patient Treatment Position and Orientation in KV Portal Images

Purpose: In the course of radiation therapy, the complex information processing workflow will Result in potential errors, such as incorrect or inaccurate patient setups. With automatic image check and patient identification, such errors could be effectively reduced. For this purpose, we developed a simple and rapid image processing method, to automatically detect the patient position and orientation in 2D portal images, so to allow automatic check of positions and orientations for patient daily RT treatments. Methods: Based on the principle of portal image formation, a set of whole body DRR images were reconstructed from multiple whole body CT volume datasets, and fused together to be used as the matching template. To identify the patient setup position and orientation shown in a 2D portal image, the 2D portal image was preprocessed (contrast enhancement, down-sampling and couch table detection), then matched to the template image so to identify the laterality (left or right), position, orientation and treatment site. Results: Five day’s clinical qualified portal images were gathered randomly, then were processed by the automatic detection and matching method without any additional information. The detection results were visually checked by physicists. 182 images were correct detection in a total of 200kV portal images. The correct rate was 91%. Conclusion: The proposed method can detect patient setup and orientation quickly and automatically. It only requires the image intensity information in KV portal images. This method can be useful in the framework of Electronic Chart Check (ECCK) to reduce the potential errors in workflow of radiation therapy and so to improve patient safety. In addition, the auto-detection results, as the patient treatment site position and patient orientation, could be useful to guide the sequential image processing procedures, e.g. verification of patient daily setup accuracy. This work was partially supported by research grant from Varian Medical System.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Advances in interpretation of subsurface processes with time-lapse electrical imaging

Electrical geophysical methods, including electrical resistivity, time-domain induced polarization, and complex resistivity, have become commonly used to image the near subsurface. Here, we outline their utility for time-lapse imaging of hydrological, geochemical, and biogeochemical processes, focusing on new instrumentation, processing, and analysis techniques specific to monitoring. We review data collection procedures, parameters measured, and petrophysical relationships and then outline the state of the science with respect to inversion methodologies, including coupled inversion. We conclude by highlighting recent research focused on innovative applications of time-lapse imaging in hydrology, biology, ecology, and geochemistry, among other areas of interest.

COMPLEX CONDUCTIVITY↗