Enabling Resilient Quantum-Secured Microgrids Through Software-Defined Networking
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Tang, Zefan↗
SEARCH · Engineering Papers
Results for “software”
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A method for crystallographic mapping of an alpha-beta titanium alloy with nanometre resolution using scanning precession electron diffraction and open-source software libraries
An approach for the crystallographic mapping of two-phase alloys on the nanoscale using a combination of scanned precession electron diffraction and open-source python libraries is introduced in this paper. This method is demonstrated using the example of a two-phase α/β titanium alloy. The data were recorded using a direct electron detector to collect the patterns, and recently developed algorithms to perform automated indexing and analyse the crystallography from the results. Very high-quality mapping is achieved at a 3 nm step size. The results show the expected Burgers orientation relationships between the α laths and β matrix, as well as the expected misorientations between α laths. A minor issue was found that one area was affected by 180° ambiguities in indexing occur due to this area being aligned too close to a zone axis of the α with twofold projection symmetry (not present in 3D) in the zero-order Laue Zone, and this should be avoided in data acquisition in the future. Nevertheless, this study demonstrates a good workflow for the analysis of nanocrystalline two- or multi-phase materials, which will be of widespread use in analysing two-phase titanium and other systems and how they evolve as a function of thermomechanical treatments.
36 MATERIALS SCIENCE↗
HiSpatialCluster: A novel high‐performance software tool for clustering massive spatial points
Abstract In the era of big data, spatial clustering is a very important means for geo‐data analysis. When clustering big geo‐data such as social media check‐in data, geotagged photos, and taxi trajectory points, traditional spatial clustering algorithms are facing more challenges. On the one hand, existing spatial clustering tools cannot support the clustering of massive point sets; on the other hand, there is no perfect solution for self‐adaptive spatial clustering. In order to achieve clustering of millions or even billions of points adaptively, a new spatial clustering tool—HiSpatialCluster—was proposed, in which the CFSFDP (clustering by fast search and finding density peaks) idea to find cluster centers and the DBSCAN (density‐based spatial clustering of applications with noise) idea of density‐connect filtering for classification are introduced. The tool’s source codes and other resources have been released on Github, and experimental evaluation was performed through clustering massive taxi trajectory points and Flickr geotagged photos in Beijing, China. The spatial clustering results were compared with those through K‐means and DBSCAN as well. As a spatial clustering tool, HiSpatialCluster is expected to play a fundamental role in big geo‐data research. First, this tool enables clustering adaptively on massive point datasets with uneven spatial density distribution. Second, the density‐connect filter method is applied to generate homogeneous analysis units from geotagged data. Third, the tool is accelerated by both parallel CPU and GPU computing so that millions or even billions of points can be clustered efficiently.
Chen, Yiran↗
Modeling of a Steam Turbine Including Partial Arc Admission for Use in a Process Simulation Software Environment
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Condensers (steam plant)↗
An open software framework for advancement of X-ray optics simulation and modeling
N/A
36 MATERIALS SCIENCE↗
Cross-platform wave optics software for XFEL applications
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36 MATERIALS SCIENCE↗
Treatment planning of a skin-sparing conical breast brachytherapy applicator using conventional brachytherapy software
Purpose: AccuBoost is a noninvasive image-guided technique for the delivery of partial breast irradiation to the tumor bed and currently serves as an alternate to conventional electron beam boost. To irradiate the target volume while providing dose sparing to the skin, the round applicator design was augmented through the addition of an internally truncated conical shield and the reduction of the source to skin distance. Methods: Brachytherapy dose distributions for two types of conical applicators were simulated and estimated using Monte Carlo (MC) methods for radiation transport and a conventional treatment planning system (TPS). MC-derived and TPS-generated dose volume histograms (DVHs) and dose distribution data were compared for both the conical and round applicators for benchmarking purposes. Results: Agreement using the gamma-index test was {>=}99.95% for distance to agreement and dose accuracy criteria of 2 mm and 2%, respectively. After observing good agreement, TPS DVHs and dose distributions for the conical and round applicators were obtained and compared. Brachytherapy dose distributions generated using Pinnacle{sup 3} for ten CT data sets showed that the parallel-opposed beams of the conical applicators provided similar PTV coverage to the round applicators and reduced the maximum dose to skin, chest wall, and lung by up to 27%, 42%, and 43%, respectively. Conclusions: Brachytherapy dose distributions for the conical applicators have been generated using MC methods and entered into the Pinnacle{sup 3} TPS via the Tufts technique. Treatment planning metrics for the conical AccuBoost applicators were significantly improved in comparison to those for conventional electron beam breast boost.
60 APPLIED LIFE SCIENCES↗
I-125 ROPES eye plaque dosimetry: Validation of a commercial 3D ophthalmic brachytherapy treatment planning system and independent dose calculation software with GafChromic{sup ®} EBT3 films
Purpose: The purpose of this study was to measure the dose distributions for different Radiation Oncology Physics and Engineering Services, Australia (ROPES) type eye plaques loaded with I-125 (model 6711) seeds using GafChromic{sup ®} EBT3 films, in order to verify the dose distributions in the Plaque Simulator™ (PS) ophthalmic 3D treatment planning system. The brachytherapy module of RADCALC{sup ®} was used to independently check the dose distributions calculated by PS. Correction factors were derived from the measured data to be used in PS to account for the effect of the stainless steel ROPES plaque backing on the 3D dose distribution.Methods: Using GafChromic{sup ®} EBT3 films inserted in a specially designed Solid Water™ eye ball phantom, dose distributions were measured three-dimensionally both along and perpendicular to I-125 (model 6711) loaded ROPES eye plaque's central axis (CAX) with 2 mm depth increments. Each measurement was performed in full scatter conditions both with and without the stainless steel plaque backing attached to the eye plaque, to assess its effect on the dose distributions. Results were compared to the dose distributions calculated by Plaque Simulator™ and checked independently with RADCALC{sup ®}.Results: The EBT3 film measurements without the stainless steel backing were found to agree with PS and RADCALC{sup ®} to within 2% and 4%, respectively, on the plaque CAX. Also, RADCALC{sup ®} was found to agree with PS to within 2%. The CAX depth doses measured using EBT3 film with the stainless steel backing were observed to result in a 4% decrease relative to when the backing was not present. Within experimental uncertainty, the 4% decrease was found to be constant with depth and independent of plaque size. Using a constant dose correction factor of T= 0.96 in PS, where the calculated dose for the full water scattering medium is reduced by 4% in every voxel in the dose grid, the effect of the plaque backing was accurately modeled in the planning system. Off-axis profiles were also modeled in PS by taking into account the three-dimensional model of the plaque backing.Conclusions: The doses calculated by PS and RADCALC{sup ®} for uniformly loaded ROPES plaques in full and uniform scattering conditions were validated by the EBT3 film measurements. The stainless steel plaque backing was observed to decrease the measured dose by 4%. Through the introduction of a scalar correction factor (0.96) in PS, the dose homogeneity effect of the stainless steel plaque backing was found to agree with the measured EBT3 film measurements.
61 RADIATION PROTECTION AND DOSIMETRY↗
Erratum: “Molecular radiotherapy: The NUKFIT software for calculating the time-integrated activity coefficient” [Med. Phys. 40, 102504 (2013)]
No abstract prepared.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
SU-E-T-253: Open-Source Automatic Software for Quantifying Biological Assays of Radiation Effects
Purpose: Clonogenic cell survival is a common assay for quantifying the effect of drugs and radiation. Manual counting of surviving colonies can take 30–90seconds per plate, a major limitation for large studies. Currently available automatic counting tools are not easily modified for radiation oncology research. Our goal is to provide an open-source toolkit for precise, accurate and fast analysis of biological assays in radiation oncology. Methods: As an example analysis, we used HeLa cells incubated with gadolinium nanoparticles prior to irradiation. After treatment, the cells are grown for 14days to allow for colony formation. To analyze the colony growth, we capture images of each dish for archiving and automatic computer-based analysis. A FujifilmX20 camera is placed at the top of a box setup, 20cm above the sample, which is backlit by a LED lamp placed at the bottom of the box. We use a Gaussian filter (width=1.3mm) and color threshold (19–255). The minimum size for a colony to be counted is 1mm. For this example, 20 dishes with a large range of colonies were analyzed. Each dish was counted 3 times manually by 3 different users and then compared to our counter. Results: Automatic counting of cell colonies takes an average of 7seconds, enabling the analysis process to be accelerated 4–12 times. The average precision of the automatic counter was 1.7%. The Student t-test demonstrated the non-significant differences between the two counting methods (p=0.64). The ICC demonstrated the reliability of each method with ICC>0.999 (automatic) and ICC=0.95 (manual). Conclusion: We developed an open-source automatic toolkit for the analysis of biological assays in radiation oncology and demonstrated the accuracy, precision and effort savings for clonogenic cell survival quantification. This toolkit is currently being used in two laboratories for routine experimental analysis and will be made freely available on our departmental website.
60 APPLIED LIFE SCIENCES↗
SU-E-T-106: An Institutional Review of Using Commercially Available Software to Evaluate Treatment Plan Quality for Various Treatment Sites and Beam Deliveries
Purpose: Use Sun Nuclear Quality Reports™ with PlanIQ™ to evaluate different treatment delivery techniques for various treatment sites. Methods: Fifteen random patients with different treatment sites were evaluated. These include the Head/Neck, prostate, pelvis, lung, esophagus, axilla, bladder and abdomen. Initially, these sites were planned on the Pinnacle {sup 3} V9.6 treatment planning system and utilized nine 6MV step-n-shoot IMRT fields. The RT plan, dose and structure sets were sent to Quality Reports™ where a DVH was recreated and the plans were compared to a unique Plan Algorithm for each treatment site. Each algorithm has its own plan quality metrics and objectives, which include the PTV coverage, PTV maximum dose, the prescription dose outside the target, doses to the critical structures, and the global maximum dose and its location. Each plan was scored base on meeting each objective. Plans may have been reoptimized and reevaluated with Quality Reports™ based on the initial score. PlanIQ™ was used to evaluate if any objective not met was achievable or difficult to obtain. A second plan using VMAT delivery was created for each patient and scored with Quality Reports™. Results: There were a wide range of scores for the different treatment sites with some scoring better for IMRT plans and some better for the VMAT deliveries. The variation in the scores could be attributed to the treatment site, location, and shape of the target. Most deliveries were chosen for the VMAT due to the short treatment times and quick patient throughput with acceptable plan scores. Conclusion: The tools are provided for both physician and dosimetrist to objectively evaluate the use of VMAT delivery versus the step-n-shoot IMRT delivery for various sites. PlanIQ validates if objectives can be met. For the physicist, a concise pass/fail report is created for plan evaluation.
60 APPLIED LIFE SCIENCES↗
SU-E-T-455: Impact of Different Independent Dose Verification Software Programs for Secondary Check
Purpose: There have been many reports for different dose calculation algorithms for treatment planning system (TPS). Independent dose verification program (IndpPro) is essential to verify clinical plans from the TPS. However, the accuracy of different independent dose verification programs was not evident. We conducted a multi-institutional study to reveal the impact of different IndpPros using different TPSs. Methods: Three institutes participated in this study. They used two different IndpPros (RADCALC and Simple MU Analysis (SMU), which implemented the Clarkson algorithm. RADCALC needed the input of radiological path length (RPL) computed by the TPSs (Eclipse or Pinnacle3). SMU used CT images to compute the RPL independently from TPS). An ion-chamber measurement in water-equivalent phantom was performed to evaluate the accuracy of two IndpPros and the TPS in each institute. Next, the accuracy of dose calculation using the two IndpPros compared to TPS was assessed in clinical plan. Results: The accuracy of IndpPros and the TPSs in the homogenous phantom was +/−1% variation to the measurement. 1543 treatment fields were collected from the patients treated in the institutes. The RADCALC showed better accuracy (0.9 ± 2.2 %) than the SMU (1.7 ± 2.1 %). However, the accuracy was dependent on the TPS (Eclipse: 0.5%, Pinnacle3: 1.0%). The accuracy of RADCALC with Eclipse was similar to that of SMU in one of the institute. Conclusion: Depending on independent dose verification program, the accuracy shows systematic dose accuracy variation even though the measurement comparison showed a similar variation. The variation was affected by radiological path length calculation. IndpPro with Pinnacle3 has different variation because Pinnacle3 computed the RPL using physical density. Eclipse and SMU uses electron density, though.
60 APPLIED LIFE SCIENCES↗
TU-PIS-Exhibit Hall-5: Use of the Enterprise-wide Dose Tracking Software Radimetrics In an Academic Medical System
The current clinical standard of organ respiratory imaging, 4D-CT, is fundamentally limited by poor soft-tissue contrast and imaging dose. These limitations are potential barriers to beneficial “4D” radiotherapy methods which optimize the target and OAR dose-volume considering breathing motion but rely on a robust motion characterization. Conversely, MRI imparts no known radiation risk and has excellent soft-tissue contrast. MRI-based motion management is therefore highly desirable and holds great promise to improve radiotherapy of moving cancers, particularly in the abdomen. Over the past decade, MRI techniques have improved significantly, making MR-based motion management clinically feasible. For example, cine MRI has high temporal resolution up to 10 f/s and has been used to track and/or characterize tumor motion, study correlation between external and internal motions. New MR technologies, such as 4D-MRI and MRI hybrid treatment machines (i.e. MR-linac or MR-Co60), have been recently developed. These technologies can lead to more accurate target volume determination and more precise radiation dose delivery via direct tumor gating or tracking. Despite all these promises, great challenges exist and the achievable clinical benefit of MRI-based tumor motion management has yet to be fully explored, much less realized. In this proposal, we will review novel MR-based motion management methods and technologies, the state-of-the-art concerning MRI development and clinical application and the barriers to more widespread adoption. Learning Objectives: Discuss the need of MR-based motion management for improving patient care in radiotherapy. Understand MR techniques for motion imaging and tumor motion characterization. Understand the current state of the art and future steps for clinical integration. Henry Ford Health System holds research agreements with Philips Healthcare. Research sponsored in part by a Henry Ford Health System Internal Mentored Grant.
60 APPLIED LIFE SCIENCES↗
A novel software and conceptual design of the hardware platform for intensity modulated radiation therapy
Purpose: To deliver high quality intensity modulated radiotherapy (IMRT) using a novel generalized sparse orthogonal collimators (SOCs), the authors introduce a novel direct aperture optimization (DAO) approach based on discrete rectangular representation. Methods: A total of seven patients—two glioblastoma multiforme, three head & neck (including one with three prescription doses), and two lung—were included. 20 noncoplanar beams were selected using a column generation and pricing optimization method. The SOC is a generalized conventional orthogonal collimators with N leaves in each collimator bank, where N = 1, 2, or 4. SOC degenerates to conventional jaws when N = 1. For SOC-based IMRT, rectangular aperture optimization (RAO) was performed to optimize the fluence maps using rectangular representation, producing fluence maps that can be directly converted into a set of deliverable rectangular apertures. In order to optimize the dose distribution and minimize the number of apertures used, the overall objective was formulated to incorporate an L2 penalty reflecting the difference between the prescription and the projected doses, and an L1 sparsity regularization term to encourage a low number of nonzero rectangular basis coefficients. The optimization problem was solved using the Chambolle–Pock algorithm, a first-order primal–dual algorithm. Performance of RAO was compared to conventional two-step IMRT optimization including fluence map optimization and direct stratification for multileaf collimator (MLC) segmentation (DMS) using the same number of segments. For the RAO plans, segment travel time for SOC delivery was evaluated for the N = 1, N = 2, and N = 4 SOC designs to characterize the improvement in delivery efficiency as a function of N. Results: Comparable PTV dose homogeneity and coverage were observed between the RAO and the DMS plans. The RAO plans were slightly superior to the DMS plans in sparing critical structures. On average, the maximum and mean critical organ doses were reduced by 1.94% and 1.44% of the prescription dose. The average number of delivery segments was 12.68 segments per beam for both the RAO and DMS plans. The N = 2 and N = 4 SOC designs were, on average, 1.56 and 1.80 times more efficient than the N = 1 SOC design to deliver. The mean aperture size produced by the RAO plans was 3.9 times larger than that of the DMS plans. Conclusions: The DAO and dose domain optimization approach enabled high quality IMRT plans using a low-complexity collimator setup. The dosimetric quality is comparable or slightly superior to conventional MLC-based IMRT plans using the same number of delivery segments. The SOC IMRT delivery efficiency can be significantly improved by increasing the leaf numbers, but the number is still significantly lower than the number of leaves in a typical MLC.
61 RADIATION PROTECTION AND DOSIMETRY↗
TU-H-CAMPUS-IeP1-02: Validation of a CT Monte Carlo Software
Purpose: To validate the in-house developed CT Monte Carlo calculation tool GMctdospp against reference simulation sets provided by the AAPM in the new report 195. Methods: Deposited energy was calculated in four segments (test 1) and two 10 cm long cylinders (test 2) inside a CTDI phantom (following case #4 of the AAPM report 195). The x-ray point source of a given 120 kVp spectrum was collimated to a fan beam with two thicknesses (10 mm, 80 mm) for a static and a rotational setup. In addition, a given chest geometry was used to calculate deposited energy in several organs for a 0° static and a rotational beam (following case #5 of the AAPM report 195). The results of GMctdospp were compared against the particular mean value of the four quoted Monte Carlo codes (EGSnrc, Geant 4, MCNP and Penelope). Results: Calculated values showed no outliers in any of the cases. Differences between GMctdospp and the particular mean Results: Calculated values showed no outliers in any of the cases. Differences between GMctdospp and the particular mean value were always at similar magnitude compared to the quoted codes. For case #4 (CTDI phantom) the relative differences were within 1.5 %, on average 0.4 % and for case #5 (chest phantom) within 2.5 % and on average 0.85 %. Conclusion: The results confirmed an overall uncertainty of the Monte-Carlo calculation chain in GMctdospp being <2.5 %, for most cases even better. This can be considered small compared to other sources of uncertainties, e.g. virtual source and patient models. The photon transport implemented in GMctdospp inside a voxel-based patient geometry was successfully verified.
60 APPLIED LIFE SCIENCES↗
TH-EF-BRB-07: Novel Hardware and Software Platform for Intermediate Energy 4π Radiotherapy
Purpose: To develop a robust and efficient platform for the optimization and robotic delivery of highly noncoplanar intensity modulated radiotherapy, which enables significant reduction of normal tissue toxicity and escalation of tumor dose. Methods: An innovative high-output compact 3 MV linac was designed for mounting onto a commercial robotic system in order to access the entire 4π beam solution space without moving the patient couch. The use of intermediate energy X-rays for radiotherapy was evaluated in comparison to clinical plans delivered using 6 MV X-rays and a state-of-the-art delivery system. Monte Carlo simulations of a 3 MV percent depth dose curve were performed for intermediate energy dose calculation. The beam model was used to create a convolution/superposition-based dose calculation engine for 3MV X-rays. The 4π greedy column generation algorithm was used for optimized beam selection and fluence map optimization. Results: A detailed design of the first 3 MV linac capable of producing a competitively high dose rate of >800 cGy/min at 100 cm was completed and verified through extensive simulation. The complete linac head including a multileaf collimator can access most of the 4π solution space including the posterior orientations without changing the couch height. When compared to 6 MV clinical plans, the proposed 3 MV 4π plans demonstrated significantly better dose compactness and normal tissue sparing in brain, prostate, and partial breast treatment plans. Conclusion: We demonstrate the design of a highly versatile radiotherapy machine to natively deliver non-coplanar 4π radiotherapy without the need to move the patient during treatment. This novel platform is efficient and capable of providing dosimetry that is 30–50% more compact than existing therapy platforms. The new system is projected to be cost effective due to improved treatment time and automation. NIH R43CA183390, NIH R01CA188300.
60 APPLIED LIFE SCIENCES↗
Delila-PY, a Pipeline for Utilizing the Delila Suite of Software to Identify Potential DNA Binding Motifs
Predicting potential DNA binding motifs is a critical part of understanding gene expression across all domains of life. Here, we report the development of Delila-PY, an easy-to-use pipeline to utilize the Delila suite to identify DNA binding motifs.
Myers, Kevin S.↗
Auto-MuRCiS: a streamlined software package for analysis of multiplex, randomized CRISPR interference sequencing data
Multiplex, randomized CRISPR interference sequencing (MuRCiS) allows for the simultaneous identification of multiple gene knockouts that together influence microbial processes. Here, we report on an updated analysis tool called Auto-MuRCiS that utilizes Docker to make the analysis of these data rapid and more user-friendly.
59 BASIC BIOLOGICAL SCIENCES↗