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At least 613 records · Page 34

Template-based CTA to x-ray angio rigid registration of coronary arteries in frequency domain with automatic x-ray segmentation

Purpose: A key challenge for image guided coronary interventions is accurate and absolutely robust image registration bringing together preinterventional information extracted from a three-dimensional (3D) patient scan and live interventional image information. In this paper, the authors present a novel scheme for 3D to two-dimensional (2D) rigid registration of coronary arteries extracted from preoperative image scan (3D) and a single segmented intraoperative x-ray angio frame in frequency and spatial domains for real-time angiography interventions by C-arm fluoroscopy.Methods: Most existing rigid registration approaches require a close initialization due to the abundance of local minima and high complexity of search algorithms. The authors' method eliminates this requirement by transforming the projections into translation-invariant Fourier domain for estimating the 3D pose. For 3D rotation recovery, template Digitally Reconstructed Radiographs (DRR) as candidate poses of 3D vessels of segmented computed tomography angiography are produced by rotating the camera (image intensifier) around the DICOM angle values with a specific range as in C-arm setup. The authors have compared the 3D poses of template DRRs with the segmented x-ray after equalizing the scales in three domains, namely, Fourier magnitude, Fourier phase, and Fourier polar. The best rotation pose candidate was chosen by one of the highest similarity measures returned by the methods in these domains. It has been noted in literature that frequency domain methods are robust against noise and occlusion which was also validated by the authors' results. 3D translation of the volume was then recovered by distance-map based BFGS optimization well suited to convex structure of the authors' objective function without local minima due to distance maps. A novel automatic x-ray vessel segmentation was also performed in this study.Results: Final results were evaluated in 2D projection space for patient data; and with ground truth values and landmark distances for the images acquired with a solid phantom vessel. Results validate that rotation recovery in frequency domain is robust against differences in segmentations in two modalities. Distance-map translation is successful in aligning coronary trees with highest possible overlap.Conclusions: Numerical and qualitative results show that single view rigid alignment in projection space is successful. This work can be extended with multiple views to resolve depth ambiguity and with deformable registration to account for nonrigid motion in patient data.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Visual Object Recognition and Tracking of Tools

A method has been created to automatically build an algorithm off-line, using computer-aided design (CAD) models, and to apply this at runtime. The object type is discriminated, and the position and orientation are identified. This system can work with a single image and can provide improved performance using multiple images provided from videos. The spatial processing unit uses three stages: (1) segmentation; (2) initial type, pose, and geometry (ITPG) estimation; and (3) refined type, pose, and geometry (RTPG) calculation. The image segmentation module files all the tools in an image and isolates them from the background. For this, the system uses edge-detection and thresholding to find the pixels that are part of a tool. After the pixels are identified, nearby pixels are grouped into blobs. These blobs represent the potential tools in the image and are the product of the segmentation algorithm. The second module uses matched filtering (or template matching). This approach is used for condensing synthetic images using an image subspace that captures key information. Three degrees of orientation, three degrees of position, and any number of degrees of freedom in geometry change are included. To do this, a template-matching framework is applied. This framework uses an off-line system for calculating template images, measurement images, and the measurements of the template images. These results are used online to match segmented tools against the templates. The final module is the RTPG processor. Its role is to find the exact states of the tools given initial conditions provided by the ITPG module. The requirement that the initial conditions exist allows this module to make use of a local search (whereas the ITPG module had global scope). To perform the local search, 3D model matching is used, where a synthetic image of the object is created and compared to the sensed data. The availability of low-cost PC graphics hardware allows rapid creation of synthetic images. In this approach, a function of orientation, distance, and articulation is defined as a metric on the difference between the captured image and a synthetic image with an object in the given orientation, distance, and articulation. The synthetic image is created using a model that is looked up in an object-model database. A composable software architecture is used for implementation. Video is first preprocessed to remove sensor anomalies (like dead pixels), and then is processed sequentially by a prioritized list of tracker-identifiers.

English, James↗

Automatic Contrail Detection and Segmentation

Automatic contrail detection is of major importance in the study of the atmospheric effects of aviation. Due to the large volume of satellite imagery, selecting contrail images for study by hand is impractical and highly subject to human error. It is far better to have a system in place that will automatically evaluate an image to determine 1) whether it contains contrails and 2) where the contrails are located. Preliminary studies indicate that it is possible to automatically detect and locate contrails in Advanced Very High Resolution Radiometer (AVHRR) imagery with a high degree of confidence. Once contrails have been identified and localized in a satellite image, it is useful to segment the image into contrail versus noncontrail pixels. The ability to partition image pixels makes it possible to determine the optical properties of contrails, including optical thickness and particle size. In this paper, we describe a new technique for segmenting satellite images containing contrails. This method has good potential for creating a contrail climatology in an automated fashion. The majority of contrails are detected, rejecting clutter in the image, even cirrus streaks. Long, thin contrails are most easily detected. However, some contrails may be missed because they are curved, diffused over a large area, or present in short segments. Contrails average 2-3 km in width for the cases studied.

Weiss, John M.↗

Labview Implementation of Image Processing and Phasing Control for the SIBOA Segmented Mirror Testbed

NASA is preparing to launch the Next Generation Space Telescope (NGST). This telescope will be larger than the Hubble Space Telescope, be launched on an Atlas missile rather than the Space Shuttle, have a segmented primary mirror, and be placed in a higher orbit. All these differences pose significant challenges.' This effort addresses the challenge of implementing an algorithm for aligning the segments of the primary mirror during the initial deployment that was designed by Philip Olivier and members of SOMTC (Space Optics Manufacturing Technology Center). The implementation was to be performed on the SIBOA (Systematic Image Based Optical Alignment) test bed. Unfortunately, hardware/software aspect concerning SIBOA and an extended time period for algorithm development prevented testing before the end of the study period. Properties of the digital camera were studied and understood, resulting in the current ability of selecting optimal settings regarding saturation. The study was successful in manually capturing several images of two stacked segments with various relative phases. These images can be used to calibrate the algorithm for future implementation. Currently the system is ready for testing.

James D. Partridge↗

Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

Plant phenotyping is typically a time-consuming and expensive endeavor, requiring large groups of researchers to meticulously measure biologically relevant plant traits, and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population scale. In this work, we address these challenges by leveraging few-shot learning with convolutional neural networks to segment the leaf body and visible venation of 2,906 Populus trichocarpa leaf images obtained in the field. In contrast to previous methods, our approach (a) does not require experimental or image preprocessing, (b) uses the raw RGB images at full resolution, and (c) requires very few samples for training (e.g., just 8 images for vein segmentation). Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools, validated using real-world physical measurements, and used to conduct a genome-wide association study to identify genes controlling the traits. In this way, the current work is designed to provide the plant phenotyping community with (a) methods for fast and accurate image-based feature extraction that require minimal training data and (b) a new population-scale dataset, including 68 different leaf phenotypes, for domain scientists and machine learning researchers. All of the few-shot learning code, data, and results are made publicly available.

59 BASIC BIOLOGICAL SCIENCES↗

WE-AB-BRA-10: Assessment of Fiber Bragg Grating (FBG)-Based Sensing for Real-Time Needle Tracking During MR-Guided Brachytherapy

Purpose: This study assesses the potential of Fiber Bragg Grating (FBG)-based sensing for real-time needle (including catheter or tube) tracking during MR-guided HDR brachytherapy. Methods: The proposed FBG-based sensing tracking approach involves a MR-compatible stylet composed of three optic fibers with nine sets of embedded FBG sensors each. When the stylet is inserted inside the lumen of the needle, the FBG sensing system can measure the needle’s deflection. For localization of the needle in physical space, the position and orientation of the stylet base are mandatory. For this purpose, we propose to fix the stylet base and determine its position and orientation using a MR-based calibration as follows. First, the deflection of a needle inserted in a phantom in two different configurations is measured during simultaneous MR-imaging. Then, after segmentation of the needle shapes on the MR-images, the position and orientation of the stylet base is determined using a rigid registration of the needle shapes on both MR and FBG-based measurements. The calibration method was assessed by measuring the deflection of a needle in a prostate phantom in five different configurations using FBG-based sensing during simultaneous MR-imaging. Any two needle shapes were employed for the calibration step and the proposed FGB-tracking approach was subsequently evaluated on the other three needles configurations. The tracking accuracy was evaluated by computing the Euclidian distance between the 3D FBG vs. MR-based measurements. Results: Over all needle shapes tested, the average(standard deviation) Euclidian distance between the FBG and MR-based measurements was 0.79mm(0.37mm). The update rate and latency of the FBG-based measurements were 100ms and 300ms respectively. Conclusion: The proposed FBG-based protocol can measure the needle position with an accuracy, precision, update rate and latency eligible for accurate needle steering during MR-guided HDR brachytherapy. M. Borot de Battisti is funded by Philips Medical Systems Nederland B.V.; M. Moerland is principal investigator on a contract funded by Philips Medical Systems Nederland B.V.; G. Hautvast and D. Binnekamp are fulltime employees of Philips Medical Systems Nederland B.V.

61 RADIATION PROTECTION AND DOSIMETRY↗

Using Heaps in Recursive Hierarchical Segmentation of Data

A modification to increase processing speed has been made in the algorithm and implementing software reported in Modified Recursive Hierarchical Segmentation of Data (GSC-14681-1), NASA Tech Briefs, Vol. 30, No. 6 (June 2006), page 51. That software performs recursive hierarchical segmentation of data having spatial characteristics (e.g., spectral-image data). The segmentation process includes an iterative subprocess, in each iteration of which it is necessary to determine a best pair of regions to merge [merges being justified by one or more measure(s) similarity of pixels in the regions]. In the previously reported version of the algorithm and software, the choice of a best pair of regions to merge involved the use of a fully sorted list of regions. That version was computationally inefficient because a fully sorted list is not needed: what is needed is only the identity of the pair of regions characterized by the smallest measure of dissimilarity. The present modification replaces the use of a fully sorted list with the use of data heaps, which are computationally more efficient for performing the required comparisons among dissimilarity measures. The modification includes the incorporation of standard and modified functions for creating and updating data heaps

Tilton, James C.↗

Flood Extent Mapping for Namibia Using Change Detection and Thresholding with SAR

A new method for flood detection change detection and thresholding (CDAT) was used with synthetic aperture radar (SAR) imagery to delineate the extent of flooding for the Chobe floodplain in the Caprivi region of Namibia. This region experiences annual seasonal flooding and has seen a recent renewal of severe flooding after a long dry period in the 1990s. Flooding in this area has caused loss of life and livelihoods for the surrounding communities and has caught the attention of disaster relief agencies. There is a need for flood extent mapping techniques that can be used to process images quickly, providing near real-time flooding information to relief agencies. ENVISAT/ASAR and Radarsat-2 images were acquired for several flooding seasons from February 2008 to March 2013. The CDAT method was used to determine flooding from these images and includes the use of image subtraction, decision based classification with threshold values, and segmentation of SAR images. The total extent of flooding determined for 2009, 2011 and 2012 was about 542 km2, 720 km2, and 673 km2 respectively. Pixels determined to be flooded in vegetation were typically <0.5 % of the entire scene, with the exception of 2009 where the detection of flooding in vegetation was much greater (almost one third of the total flooded area). The time to maximum flooding for the 2013 flood season was determined to be about 27 days. Landsat water classification was used to compare the results from the new CDAT with SAR method; the results show good spatial agreement with Landsat scenes.

Flood↗

Summary Statistics for LC_TA03_130719: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, lithium carbonate (LC). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, LC_TA03_130719, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images 2 . The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MP03_130620: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MP03_130620, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images 2 . The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MH03_130828: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MH03_130828, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MH01_130826: Micro-CT Data Acquired at LLNL, Specimen 1 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MH01_130826, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MH02_130827: Micro-CT Data Acquired at LLNL, Specimen 2 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MH03_130827, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MC03_130806: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MC03_130806, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MC02_130701: Micro-CT Data Acquired at LLNL, Specimen 2 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MC02_130701, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_ST01_130731: Micro-CT Data Acquired at LLNL, Specimen 1 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_ST01_130731, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_SH02_130820: Micro-CT Data Acquired at LLNL, Specimen 2 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_SH02_130820, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗

Summary Statistics for TA_MT03_130730: Micro-CT Data Acquired at LLNL, Specimen 3 of 3

Using x-ray micro computed tomography (MicroCT), we have characterized the linear attenuation coefficients (LAC), μ, of a sample of a dry powder material, tartaric acid (TA). The specimen was prepared at Lawrence Livermore National Laboratory (LLNL), loaded into a 60mL low density polyethylene (LDPE) bottle. After completed packing, the specimen was scanned following the protocol for MicroCT measurements under Test Plan 79. This particular specimen, TA_MT03_130730, recorded the bulk packing density (mass of sample divided by volume of sample) shown above. Two additional preparations were made and analyzed. We used the computer program IMGREC to reconstruct the CT images. The values of the key parameters used in the x-ray data capture and image reconstruction are given in this report. Additional experimental details may be found in the SOP and a separate document. To characterize the statistical distribution of LAC values in each CT image, we first isolated an ~80% region or segment of volume elements (“voxels”) lying completely within the sample, away from the walls of the container. We then calculated the mean value, standard deviation and entropy for (a) the high and low energy image segments and for (b) their digital gradient images. The statistics of the initial image of LAC values are called “first order statistics;” those of the gradient image, “second order statistics.” See Seetho for details of the analysis used to obtain the numbers reported in this document.

42 ENGINEERING↗