Overlay Tool Research Articles

SU-D-105-01: Patient-Specific Quality Assurance for Monte Carlo-Calculated Lung SBRT On Cyberknife - Is It Necessary?

Purpose: In transitioning from ray-tracing (RT) to Monte Carlo (MC) dose computation algorithm for Cyberknife lung stereotactic body radiotherapy (SBRT), we realized large differences (10–20%) in PTV coverage to heterogeneous target regions which required dosimetric confirmation. Currently, our practice requires an independent second calculation for all plans. MuCheck software (Oncology Data Systems) is used in lieu of physical measurements for RT plans; however, there exists no commercial software for verifying MC plans. We determined all lung SBRT plans should utilize the MC algorithm and initially be confirmed by direct measurements. Methods: Lung treatment plans were first optimized with RT then recalculated using MC for final optimization and high-resolution dose computation. The MC plan was superimposed on a heterogeneous thorax phantom CT (Standard Imaging 91230) using the phantom overlay tool of the MultiPlan 3.5.2 software. Isodose distributions were manually shifted to place the ion chamber (0.053cc Exradin-A1SL) in a suitably homogeneous region within the CTV. The plan was then delivered to the thorax phantom with the ion chamber placed in the mediastinum insert location. Results: This methodology was used for 33 consecutive lung patients receiving Cyberknife SBRT with PTVs ranging from 10.7–185.9cm3. The mean deviation between measured and MC calculated doses was −2.31%±1.66%. The maximum deviation was −4.69%. Acceptable tolerance for patient-specific QA was considered ±5%. Conclusion: The MC algorithm provides improved accuracy over RT for heterogeneous dose calculation, confirmed by direct point measurements. Patient-specific QA using a heterogeneous lung phantom provided an acceptable anthropomorphic approximation of patient plans calculated with MC. Since the QA results establish satisfactory delivery of MC doses, patient-specific plans calculated on a homogeneous phantom comparing RT and MC algorithms may provide a suitable second check without direct measurement. Conversely, many users may continue direct measurement as a second check until commercial MC verification software becomes available.

Application of DRASTIC Model based on Entropy Weight to the Assessment on Vulnerability of Groundwater in Weining Plain

Given the weight in groundwater vulnerability assessment, entropy weight combined with DRASTIC model is considered to assess the groundwater vulnerability. The assessment index weight is assessed by entropy weight and the model is ultimately applied to the assessment on the vulnerability of the groundwater in Weining Plain of Ningxia Hui Autonomous Region. Firstly, based on the seven assessment index attribute partition charts, the assessment index weight is calculated by entropy weight; then, by the ARCGIS grid image overlay tool to overlay the seven index grid images, the composite index chart of the assessment on the vulnerability of the groundwater in the study area is developed; finally, according to the classification standard, a partition chart of the assessment on the vulnerability of the groundwater in the study area is made to carry out the result analysis of the assessment on the vulnerability of the groundwater in the study area. The comprehensive assessment results indicate that the application of entropy weight to the DRASTIC model is feasible and the assessment results are more objective and direct.

A grid overlay framework for analysis of medical images and its application to the measurement of stroke lesions

To create and evaluate an interactive software tool for measuring imaging data in situations where hand-drawn region-of-interest measurements are unfeasible, for example, when the structure of interest is patchy with ill-defined boundaries. An interactive grid overlay software tool was implemented that enabled coding of voxels dependent on their imaging appearance with a series of user-defined classes. The Grid Analysis Tool (GAT) was designed to automatically extract quantitative imaging data, grouping the results by tissue class. Inter- and intra-observer reproducibility was evaluated by six observers of various backgrounds in a study of acute stroke patients. The software tool enabled a more detailed classification of the stroke lesion than would be possible with a region-of-interest approach. However, inter-observer coefficients of variation (CVs) were relatively high, reaching 70% in "possibly abnormal" tissue and around 15-20% in normal appearing tissues, while intra-observer CVs were no more than 13% in "possibly abnormal" tissue and generally less than 1% in normal-appearing tissues. The grid-overlay method overcomes some of the limitations of conventional Region Of Interest (ROI) approaches, providing a viable alternative for segmenting patchy lesions with ill-defined boundaries, but care is required to ensure acceptable reproducibility if the method is applied by multiple observers. Computer software developed to overcome limitations of conventional regions of interest measurements • This software is suitable for patchy lesions with ill-defined borders • Allows a more detailed assessment of imaging data.

Processing moldable tasks on the grid: Late job binding with lightweight user-level overlay

Independent observations and everyday user experience indicate that performance and reliability of large grid infrastructures may suffer from large and unpredictable variations. In this paper we study the impact of the job queuing time on processing of moldable tasks which are commonly found in large-scale production grids. We use the mean value and variance of makespan as the quality of service indicators. We develop a general task processing model to provide a quantitative comparison between two models: early and late job binding in a user-level overlay applied to the EGEE Grid infrastructure. We find that the late-binding model effectively defines a transformation of the distribution of makespan according to the Central Limit Theorem. As demonstrated by Monte Carlo simulations using real job traces, this transformation allows to substantially reduce the mean value and variance of makespan. For certain classes of applications task granularity may be adjusted such that a speedup of an order of magnitude or more may be achieved. We use this result to propose a general strategy for managing access to resources and optimization of workload based on Ganga and DIANE user-level overlay tools. Key features of this approach include: a late-binding scheduler, an ability to interface to a wide range of distributed systems, an ability to extend and customize the system to cover application-specific scheduling and processing patterns and finally, ease of use and lightweight deployment in the user space. We discuss the impact of this approach for some practical applications where efficient processing of many tasks is required to solve scientific problems.

Selection of suitable areas for rubber tree (Hevea brasiliensi) plantation using GIS‐data in Laos

The Lao government has a policy of promoting Laos to become a leading rubber exporter in the world market by the year 2020. However, the implementation showed serious problems in terms of land allocation. Land leased to investors overlapped with farmlands of local people, creating conflicts between local people and investors, as well as between local people and local government authorities. In addition, the concession of areas without previous forestry survey has led to massive deforestations. These problems demonstrated that the local government needs to plan for and implement good land use management strategies. The aim of this study is not only to identify suitable areas for rubber tree (Hevea brasiliensis) plantation (SARTP) but also areas for forest and agriculture to model sustainable land use management in local areas. The study area conducted in Pakxong District, southern part of Laos, which total area covers approximately 345,545 ha, with forest covering about 232,721 ha. The geography database such as land use type; forest types; digital elevation model (DEM) resolution with 50m and soil characteristic were used integrate geographic information system (GIS) technique. Multi‐Criteria Evaluation (MCE) and restriction for producing suitable maps based on geographic data was defined. These information combines with overlay tools and weight overlay processing identify a land and forest allocation map, which includes SARTP, as well as a forest functions and agriculture area map.

Subnanometer-accuracy z-position monitor mask for optical lithography

A lithographic test pattern, the phase shift grating (PSG) z monitor, is introduced. Through the use of phase shift techniques, position errors of images in the z-direction translate into lateral shifts in the printed pattern. The lateral shifts are easily measurable using an overlay metrology tool. Each z monitor pattern in a test mask can be directly read for the sign and magnitude of the z error. When the experimental conditions, namely, the period of a PSG and a coherent factor of the lithography tool simultaneously satisfies a criterion of the asymmetric two-beam interference between the zeroth-order ray and either of the two first-order rays of diffraction, the linearity of a z-vs-overlay curve is always complete and the slope of the curve is constant everywhere in the image field. Using state-of-the-art overlay metrology tools, we realized subnanometer-order accuracy in the z measurement.

Abdominal Wall CT Angiography: A Detailed Account of a Newly Established Preoperative Imaging Technique

Institutional review board approval was obtained for this study, and all patients gave written informed consent. Autologous surgical breast reconstruction with use of abdominal wall donor flaps based on the deep inferior epigastric artery (DIEA) and one or more of its anterior musculocutaneous perforating branches (DIEA perforator flap) is being used with increasing frequency instead of breast reconstruction with use of traditional transverse rectus abdominus musculocutaneous and modified muscle-sparing flaps. Preoperative mapping of the DIEA perforators with abdominal wall computed tomographic (CT) angiography may improve patient care by providing the surgeon with additional information that will lead to optimization of the surgical technique, shorter procedure time, and reduction in the frequency of surgical complications. The branching patterns of the DIEA, the segmental anatomy of the anterior adipocutaneous perforating branches of the DIEA, and the importance of these features in pre- and intraoperative surgical planning necessitate a different approach to abdominal wall CT angiography than that used with other abdominal CT angiographic techniques. In abdominal wall CT angiography, the common femoral artery is used as the bolus trigger, CT scanning is performed in the caudocranial direction, the automatic exposure control feature is disabled, a scaled grid overlay tool is used to present information to the surgeons, and radiation dose is minimized (average dose, 6 mSv). The anatomic accuracy of abdominal wall CT angiography has been investigated in cadaveric and surgical studies, with sensitivity of 96%-100% and specificity of 95%-100%. This detailed description will allow other radiologists and surgeons interested in free DIEP flap surgery to incorporate this useful tool into their practice.

A geographic information system to study trauma epidemiology in India

BackgroundGeographic Information Systems (GIS) describe the topography and chronology of events in a defined vector space. GIS may also be used for an integrated analysis of environmental and road-related risk factors for traffic accidents.MethodsIn a retrospective study, various features of 165 road crashes were linked to a GIS-generated digital map of an area close to a national highway in India. By overlay tools, clusters of accidents were identified, and color-coded according to accident mechanisms and injury patterns.ResultsSpatial analysis revealed a cluster with a high incidence of motorbike injuries resulting in fractures. Examination of the spot demonstrated the risky combination of a speed breaker and a broken traffic light. After fixing the light, no further accidents occurred at the site.ConclusionGIS is a promising technology for geo-referencing accident data, and may be a valuable tool to identify areas of priority for injury prevention in India.

Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changes

Copy number abnormalities (CNAs) in tumor cells are presumed to affect expression levels of genes located in region of abnormality. To investigate this relationship we have surveyed the losses, gains and amplifications in 30 glioblastomas using array comparative genome hybridization and compared these data with gene expression changes in the same tumors using the Affymetrix U133Plus2.0 oligonucleotide arrays. The two datasets were overlaid using our in-house overlay tool which highlights concordance between CNAs and expression level changes for the same tumors. In this survey we have highlighted genes frequently overexpressed in amplified regions on chromosomes 1, 4, 11, and 12 and have identified novel amplicons on these chromosomes. Deletions of specific regions on chromosomes 9, 10, 11, 14, and 15 have also been correlated with reduced gene expression in the regions of minimal overlap. In addition we describe a novel approach for comparing gene expression levels between tumors based on the presence or absence of chromosome CNAs. This genome wide screen provides an efficient and comprehensive survey of genes which potentially serve as the drivers for the CNAs in GBM.

SU‐FF‐J‐21: A Comparison of a Point Based Tool with An Image Overlay Tool for Fiducial Based Setup

Purpose: To compare interactive image overlay tools for fiducial based setup with a point based system. Method and Materials: A single implanted fiducial was used for localization. Gated kVp images were acquired for daily setup; if a shift was made, a 2nd set of images were acquired subsequent to the shift. Shifts were determined using both a commercial software package designed for point matching (ISOLOC, CIVCO, Kalona, IA) and also by dragging the projection of the fiducial contour over the image of the fiducial using tools integrated into the treatment delivery console(4DTC, Varian, Palo Alto, CA). Data was collected for 29 shifts on 15 different days. Results: The mean magnitude of the initial shifts were 1.5, 5.7, and 1.5 mm and the means of the differences between the shifts were 0.2, 1.1 and 0.8 mm in the lateral, cranial‐caudal, and AP directions respectively. On many days there was a discrepancy of 1–2 mm between the AP and lateral gated kVp X‐rays. The interactive tools allowed the user to compromise between the two projections, while the automatic system forced a compromise. The interactive tools also displayed a projection of the tumor allowing validation of the position of the fiducial with respect to the bulk tumor. The interactive tools were quicker to use and automatically applied the shifts; these tools are somewhat limited by the accuracy of the contouring of the fiducials. Conclusion: Both the interactive tools and the automatic system are practical for daily setup of patients with fiducials, but the integration into the console, the speed of localization, and most importantly the ability to correlate the fiducials with radioopaque anatomy make the interactive tools superior.

Aberration evaluation of alignment optics in lithographic tools by use of a step-height structure highly sensitive to the asymmetry of an optical image

To satisfy the increasing demand for extremely tight overlay accuracy in semiconductor manufacturing processes, all the measurement error factors in alignment systems and overlay measurement tools need be identified and eliminated. The principle of most alignment systems is based on image processing of target marks on the wafer under bright-field illumination. Although the phenomenon that the sensitivity to the alignment error varies with the step height (SH) of the mark has been known and used for evaluating the performance of the alignment optics, no investigation has been made into the origin and the physical mechanism of the phenomenon. We propose a simplified optical model that can account for the origin of the asymmetric image and clarify its relation to the SHs. The model is validated with simulation and experimental results. The improved performance of an alignment system using marks with optimally designed SHs is demonstrated.

Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms

The Overlay Tool© has been developed to combine high throughput data derived from various microarray platforms. This tool analyzes high-resolution correlations between gene expression changes and either copy number abnormalities (CNAs) or loss of heterozygosity events detected using array comparative genomic hybridization (aCGH). Using an overlay analysis which is designed to be performed using data from multiple microarray platforms on a single biological sample, the Overlay Tool© identifies potentially important genes whose expression profiles are changed as a result of losses, gains and amplifications in the cancer genome. In addition, the Overlay Tool© will incorporate loss of heterozygosity (LOH) probability data into this overlay procedure. To facilitate this analysis, we developed an application which computationally combines two or more high throughput datasets (e.g. aCGH/expression) into a single categorized dataset for visualization and interrogation using a gene-centric approach. As such, data from virtually any microarray platform can be incorporated without the need to remap entire datasets individually. The resultant categorized (overlay) data set can be conveniently viewed using our in-house visualization tool, aCGHViewer© (Shankar et al. 2006), which serves as a conduit to public databases such as UCSC and NCBI, to rapidly investigate genes of interest.

Overlay analysis of the oligonucleotide array gene expression profiles and copy number abnormalities as determined by array comparative genomic hybridization in medulloblastomas

Combined analysis of gene expression array data and array-based comparative genomic hybridization data have been used in a series of 26 pediatric brain tumors to define up- and downregulated genes that coincide with losses, gains, and amplifications involving specific chromosome regions. Frequent losses were defined in chromosome arms 3q, 6q, 8p, 10q, 16q, 17p, and gains were identified in chromosome 7, and chromosome arms 9p and 17q. Amplification of a 2p region was seen in only one tumor, which corresponded to increased expression of the MYCN and DDX1 genes. To facilitate the analysis of the two data sets, we have developed a custom overlay tool that defines genes that are underexpressed in regions of deletions and overexpressed in regions of gain, across the genome and specifically within regions showing recurrent involvement in medulloblastomas.

Image placement error: closing the gap between overlay and imaging

We perform experimental and theoretical studies of image placement error induced by aberrations of the projection lens. The goal is to experimentally determine the magnitude of the image placement errors, to compare experiments and simulations, and to screen possible correction strategies. The calculations and experiments are done for ArF lithography. Theoretically, we simulate image placement error using the projection lens aberration data and simulators such as Prolith or Solid-C. Features with low and high sensitivities to lens aberrations are identified, together with a reference feature that has low sensitivity for image placement error. Dedicated reticles are fabricated to print various features at different illumination conditions on the same substrate. The resulting patterns could be analyzed using top-down scanning electron microscopy (SEM), but also optically with the standard optical overlay tool KLA5200. For both techniques, the experimentally found image placement errors are in excellent agreement with simulations. In simulations, we calculate the dependency of the image placement error on pattern density, pattern orientation, and illumination conditions. These tendencies are experimentally reproduced. We conclude with a case study that demonstrates a possible correction strategy for image placement error.

Image displacement sensing (NDSE) for achieving overlay alignment

In this paper we discuss the application of NDSE [1] (Hewlett Packard’s nanoscale displacement sensing and estimation technology) as an overlay metrology tool. We describe a method where nanoscale displacement sensing forms the basis of a precision alignment measurement. We will then provide a review of experiments performed to assess the accuracy of one particular NDSE algorithm, tracking silicon targets as they translate on a piezoelectric stage under an optical microscope. We conclude by describing upcoming experiments which will incorporate NDSE as an alignment sensor in a nanoimprint lithography application.

USING GIS AND EARTHQUAKE SCENARIOS FOR THE ASSESSMENT OF EMERGENCY RESPONSE IN CASE OF A STRONG EARTHQUAKE. AN APPLICATION IN THE URBAN AREA OF THESSALONIKI, GREECE

The aim of this paper, which is part of the M.Sc Thesis of the first author, is an initial attempt for the assessment of the emergency response through the road network of the Urban Area of Thessaloniki (UAT) after a strong earthquake. The areas of the road network that are to become inaccessible either due to partial collapse of buildings or due to destruction of the road axes by rupture zones, are detected. The inaccessible parts are determined for the cases of three earthquake scenarios using the values of the Peak Ground Acceleration (PGA), which were calculated for about 6000 points over the UAT, as well as spatial overlay tools of a GIS. In the end, by applying network analysis and according to the situation of the network after the earthquake, the possibility of movement of the fire engines and ambulances was studied and least cost routes from ambulance stations to UAT hospitals were tracked.

Measurement of Wave-Front Aberrations in Lithography Lenses with an Overlay Inspection Tool

Measurement methods using overlay inspection tools have been established for wave-front aberrations in optical lithography lenses used for integrated circuit manufacturing. Three-beam interferometry and asymmetric two-beam interferometry can transform the wave-front aberrations at selected points on the lens pupil to lateral image shifts for fine grating objects. A technique of overlapped exposures makes the image shifts of inner lines of the grating images optically measurable, even if the images are too fine to be resolved optically. These methods are available in the fields of integrated circuit manufacturing and lithography tool assembling. This paper sums up measurement methods for wave-front aberrations. It is experimentally estimated that the methods are equally matched with the phase measuring interferometry widely used in the tool assemblies respecting accuracy and precision.

Applications in neuroscience of a computer based talairach overlay tool

Applications in neuroscience of a computer based talairach overlay tool

Aberration measurement from specific photolithographic images: a different approach

Techniques for measurement of higher-order aberrations of a projection optical system in photolithographic exposure tools have been established. Even-type and odd-type aberrations are independently obtained from printed grating patterns on a wafer by three-beam interference under highly coherent illumination. Even-type aberrations, i.e., spherical aberration and astigmatism, are derived from the best focus positions of vertical, horizontal, and oblique grating patterns by an optical microscope. Odd-type aberrations, i.e., coma and three-foil, are obtained by detection of relative shifts of a fine grating pattern to a large pattern by an overlay inspection tool. Quantitative diagnosis of lens aberrations with a krypton fluoride (KrF) excimer laser scanner is demonstrated.

Focus characterization using end of line metrology

A new method is introduced to measure relative focus using conventional optical overlay instruments. Optical end of line metrology (OELM), is based on patterning a wide frame in which adjacent sides are constructed of submicron sized lines that run perpendicular to the center opening. Because truncation is size dependent, line and space features exhibit significantly more line shortening effects than the solid sections. When measured with a conventional optical overlay tool, the difference in line shortening between the solid and line and space sections are measured as an alignment offset, which is a relative measure of actual line shortening. Reproducibility for measuring the apparent misalignment of these modified box-in-box structures was 3 nm (3/spl sigma//sup est/), which is similar to the repeatability for measuring conventional resist box in box alignment boxes. Truncation is sensitive to focus and the utility for using OELM toward characterizing focus-dependent lens parameters was investigated. Estimated 3/spl sigma/ for calculating best focus and astigmatism were 0.04 /spl mu/m and 0.01 /spl mu/m, respectively. Focus corrections were accurate to 0.05 /spl mu/m within /spl plusmn/0.3 /spl mu/m of best focus. Additionally, a general method is presented to estimate the error in the calculated best focus.