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Articles 1 - 26 of 26

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

A New Method For Shear Wave Speed Estimation In Shear Wave Elastography, Aaron J. Engel, Gregory R. Bashford Dec 2015

A New Method For Shear Wave Speed Estimation In Shear Wave Elastography, Aaron J. Engel, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Visualization of mechanical properties of tissue can aid in noninvasive pathology diagnosis. Shear wave elastography (SWE) measures the elastic properties of soft tissues by estimation of local shear wave propagation speed. In this paper, a new robust method for estimation of shear wave speed is introduced which has the potential for simplifying continuous filtering and real-time elasticity processing. Shear waves were generated by external mechanical excitation and imaged at a high frame rate. Three homogeneous phantoms of varying elastic moduli and one inclusion phantom were imaged. Waves propagating in separate directions were filtered and shear wave speed was estimated by ...


Functional Transcranial Doppler Ultrasound For High Temporal Resolution Measurement Of Lateralization In Visual Memory And Visual Search Cognitive Tasks, B. Hage, M. Alwatban, E. Barney, M. Mills, M. Dodd, E. Truemper, Gregory R. Bashford Jan 2015

Functional Transcranial Doppler Ultrasound For High Temporal Resolution Measurement Of Lateralization In Visual Memory And Visual Search Cognitive Tasks, B. Hage, M. Alwatban, E. Barney, M. Mills, M. Dodd, E. Truemper, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Functional transcranial Doppler ultrasound (fTCD) is a noninvasive sensing modality that measures blood flow velocities in cerebral arteries (CBFV) with high temporal resolution. Few studies have examined the relationship of CBFV change during visual search and visual memory cognitive tasks. Here a protocol to compare lateralization between these two similar tasks using fTCD is demonstrated. Thirteen healthy volunteers were shown visual scenes on a computer and performed visual search and visual memory tasks while CBFV in the bilateral middle cerebral arteries was monitored with fTCD. Each subject completed 40 trials, consisting of baseline, calibration, instruction, and task periods. Lateralization was ...


Enabling Real-Time Ultrasound Imaging Of Soft Tissue Mechanical Properties By Simplification Of The Shear Wave Motion Equation, Aaron J. Engel, Gregory R. Bashford Jan 2015

Enabling Real-Time Ultrasound Imaging Of Soft Tissue Mechanical Properties By Simplification Of The Shear Wave Motion Equation, Aaron J. Engel, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Ultrasound based shear wave elastography (SWE) is a technique used for non-invasive characterization and imaging of soft tissue mechanical properties. Robust estimation of shear wave propagation speed is essential for imaging of soft tissue mechanical properties. In this study we propose to estimate shear wave speed by inversion of the firstorder wave equation following directional filtering. This approach relies on estimation of first-order derivatives which allows for accurate estimations using smaller smoothing filters than when estimating second-order derivatives. The performance was compared to three current methods used to estimate shear wave propagation speed: direct inversion of the wave equation (DIWE ...


Flowcell Systems For Single Molecule Detection, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff Apr 2012

Flowcell Systems For Single Molecule Detection, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.


Two-Dimensional Blood Flow Velocity Estimation Using Apparent Speckle Pattern Angle Dependence On Scan Velocity, Tiantian Xu, Gregory R. Bashford Jan 2012

Two-Dimensional Blood Flow Velocity Estimation Using Apparent Speckle Pattern Angle Dependence On Scan Velocity, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An algorithm which measures the lateral component of blood flow velocity was developed in our previous studies based on the increase in speckle size due to relative motion between moving scatterers and spatial rate of scanner A-line acquisition (scan velocity). In this paper, the apparent dominant angle of the speckle pattern in a straight vessel was investigated and a new method of two-dimensional blood flow velocity estimation is introduced. Different scan velocities were used for data acquisition from blood flow traveling at an angle relative to the ultrasound beam. The apparent angle of the speckle pattern changes with different scan ...


Monitoring Cerebral Hemodynamics With Transcranial Doppler Ultrasound During Cognitive And Exercise Testing In Adults Following Unilateral Stroke, Brian P. Watt, Judith M. Burnfield, Edward J. Truemper, Thad W. Buster, Gregory R. Bashford Jan 2012

Monitoring Cerebral Hemodynamics With Transcranial Doppler Ultrasound During Cognitive And Exercise Testing In Adults Following Unilateral Stroke, Brian P. Watt, Judith M. Burnfield, Edward J. Truemper, Thad W. Buster, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An observational study was performed as a preliminary investigation into the use of transcranial Doppler ultrasound (TCD) for recording cerebral hemodynamic changes during multiple tasks. TCD is a method of measuring cerebral blood flow (CBF) using ultrasound transducers in contact with the surface of the head. Using the maximum flow envelope of the Doppler spectrum returning from the middle cerebral artery (MCA), standard clinical flow indices can be calculated and displayed in real time providing information concerning perturbations in CBF and their potential cause. These indices as well as flow velocity measurements have been recognized as useful in measuring changes ...


Lateral Blood Flow Velocity Estimation Based On Ultrasound Speckle Size Change With Scan Velocity, Tiantian Xu, Gregory R. Bashford Dec 2010

Lateral Blood Flow Velocity Estimation Based On Ultrasound Speckle Size Change With Scan Velocity, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional (Doppler-based) blood flow velocity measurement methods using ultrasound are capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. A new method has been introduced which estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to blood reflectors (typically red blood cells) stretches (i.e., is smeared ...


Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff Feb 2010

Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.


Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi Reynolds, Pamela Sheaff Dec 2009

Charge Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charged-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.


Further Progress On Lateral Flow Estimation Using Speckle Size Variation With Scan Direction, Tiantian Xu, Gregory R. Bashford Jan 2009

Further Progress On Lateral Flow Estimation Using Speckle Size Variation With Scan Direction, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional blood flow velocity measurement using ultrasound is capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these Doppler-based methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. In this paper, we report additional data on a new method recently introduced. This method estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to the blood reflectors (typically ...


Resolving The Lateral Component Of Blood Flow Velocity Based On Ultrasound Speckle Size Change With Scan Direction And Speed, Tiantian Xu, Greg R. Bashford Jan 2009

Resolving The Lateral Component Of Blood Flow Velocity Based On Ultrasound Speckle Size Change With Scan Direction And Speed, Tiantian Xu, Greg R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Conventional blood flow velocity measurement using ultrasound is capable of resolving the axial component (i.e., that aligned with the ultrasound propagation direction) of the blood flow velocity vector. However, these Doppler-based methods are incapable of detecting blood flow in the direction normal to the ultrasound beam. In addition, these methods require repeated pulse-echo interrogation at the same spatial location. In this paper, we introduce a method which estimates the lateral component of blood flow within a single image frame using the observation that the speckle pattern corresponding to the blood reflectors (typically red blood cells) stretches (i.e., is ...


Single Molecule Diffusion Coefficient Estimation By Image Analysis Of Simulated Ccd Images To Aid High-Throughput Screening, Pengfei Song, Lloyd M. Davis, Greg Bashford Jan 2009

Single Molecule Diffusion Coefficient Estimation By Image Analysis Of Simulated Ccd Images To Aid High-Throughput Screening, Pengfei Song, Lloyd M. Davis, Greg Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Extension of one-dimensional signal analysis to two-dimensional image analysis could accelerate conventional methods of high-throughput screening in the discovery of new pharmaceutical agents. This work describes a first step taken towards this goal – the evaluation of image-analysis based estimation strategies of the diffusion coefficient of a single molecule transported within a microfabricated flowcell. A computer simulation of single-molecule imaging by a charge-coupled device (CCD) camera is used to determine if it is possible to distinguish three different types of molecules with different diffusion coefficients. The Gaussian fitting algorithm finds the variance of the transverse trajectory, which increases linearly with the ...


Optimal Thresholds Of Feature Tracking For Blood Velocity And Tissue Motion Estimation, Tiantian Xu, Gregory R. Bashford Jan 2009

Optimal Thresholds Of Feature Tracking For Blood Velocity And Tissue Motion Estimation, Tiantian Xu, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

Feature tracking is an algorithm for estimating blood flow velocity and tissue motion using pulse-echo ultrasound. In contrast to cross-correlation speckle-tracking techniques, feature tracking identifies features at discrete locations and corresponds them from frame to frame. Prior studies have demonstrated that feature-tracking estimates exhibit lower variance than those obtained by the conventional autocorrelation method and require less computational complexity than either speckle tracking or autocorrelation. To date, not much attention has been paid to the process by which trackable features (normally local maxima) are selected from the set of all available features. In the selection process, it is desired to ...


Tendinopathy Discrimination By Use Of Spatial Frequency Parameters In Ultrasound B-Mode Images, Gregory R. Bashford, Nicholas Tomsen, Shruti Arya, Judith M. Burnfield, Kornelia Kulig May 2008

Tendinopathy Discrimination By Use Of Spatial Frequency Parameters In Ultrasound B-Mode Images, Gregory R. Bashford, Nicholas Tomsen, Shruti Arya, Judith M. Burnfield, Kornelia Kulig

Biomedical Imaging and Biosignal Analysis Laboratory

The structural characteristics of a healthy tendon are related to the anisotropic speckle patterns observed in ultrasonic images. This speckle orientation is disrupted upon damage to the tendon structure as observed in patients with tendinopathy. Quantification of the structural appearance of tendon shows promise in creating a tool for diagnosing, prognosing, or measuring changes in tendon organization over time. The current work describes a first step taken towards this goal—classification of Achilles tendon images into tendinopathy and control categories. Eight spatial frequency parameters were extracted from regions of interest on tendon images, filtered and classified using linear discriminant analysis ...


Direct Comparison Of Feature Tracking And Autocorrelation For Velocity Estimation, Gregory R. Bashford, Derek J. Robinson Apr 2007

Direct Comparison Of Feature Tracking And Autocorrelation For Velocity Estimation, Gregory R. Bashford, Derek J. Robinson

Biomedical Imaging and Biosignal Analysis Laboratory

Feature tracking is an algorithm for estimating tissue motion and blood flow using pulse-echo ultrasound. It was proposed as a computationally simpler alternative to other techniques such as autocorrelation and time-domain cross correlation. The advantage of feature tracking is that it selectively extracts easily identifiable parts of the speckle signal (e.g., the local maxima), reducing the amount of information being processed. Studies on feature tracking to date have used stationary, specklegenerating targets to simulate blood flow. Also, feature tracking has not been compared with accepted commercial methods. This study directly compares feature tracking performance with the complex autocorrelation method ...


Single Molecule Detection Systems And Methods, John G. K. Williams, Gregory R. Bashford Oct 2006

Single Molecule Detection Systems And Methods, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

A micofluidic system is provided that includes a substrate, a first microchannel disposed in the substrate for providing a reactant to a reaction zone, a second microchannel disposed in the substrate, the third microchannel providing fluid communication between the first and second microchannels. The system also typically includes first and second electrodes, positioned at opposite ends of the second microchannel, for providing an electric field within the second microchannel. In operation, when the reactant is in the reaction zone, a reaction product is produced having a net electric charge different from the electric of the reactant.


Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff Aug 2005

Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford, Jiyan Chen, Dan Draney, Nara Narayanan, Bambi L. Reynolds, Pamela Sheaff

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation Without interference from unincorporated NPs and Without illuminating the polymerase-DNA complex.


Nucleic Acid Sequencing Using Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford Mar 2005

Nucleic Acid Sequencing Using Charge-Switch Nucleotides, John G. K. Williams, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

The present invention provides compounds, methods and systems for sequencing nucleic acid using single molecule detection. Using labeled NPs that exhibit charge-switching behavior, single-molecule DNA sequencing in a microchannel sorting system is realized. In operation, sequencing products are detected enabling real-time sequencing as successive detectable moieties flow through a detection channel. By electrically sorting charged molecules, the cleaved product molecules are detected in isolation without interference from unincorporated NPs and without illuminating the polymerase-DNA complex.


Imposed Constraints On The Smith-Waterman Alignment Algorithm For Enhanced Modeling Of A Single-Molecule Dna Sequencer, Patrick G. Humphrey, Gregory R. Bashford Jan 2005

Imposed Constraints On The Smith-Waterman Alignment Algorithm For Enhanced Modeling Of A Single-Molecule Dna Sequencer, Patrick G. Humphrey, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An effort has been underway to develop a system for de novo sequencing of single DNA molecules with very long reads. The system operates by optically detecting the passage of fluorescently tagged DNA bases through a detection zone. A successful system would be revolutionary with respect to speed, read length, cost and minimized laboratory infrastructure. An important part of system development is modeling of the detection process. In particular, predicting the expected error from a set of sequencing parameters is helpful in system design. This paper describes variations on the Smith-Waterman algorithm for subsequence alignment used in a single-molecule detection ...


Flash Artifact Suppression In Two-Dimensional Ultrasound Imaging, Richard Yung Chiao, Gregory Ray Bashford, Mark Peter Feilen, Cynthia Andrews Owen Jul 2004

Flash Artifact Suppression In Two-Dimensional Ultrasound Imaging, Richard Yung Chiao, Gregory Ray Bashford, Mark Peter Feilen, Cynthia Andrews Owen

Biomedical Imaging and Biosignal Analysis Laboratory

Flash artifacts in ultrasound flow images are suppressed to achieve enhanced flow discrimination. Flash artifacts typically occur as region of elevated signal strength (brightness or equivalent color) within an image. A flash suppression algorithm included the steps of estimating the flash within an image and then suppressing the estimated flash. The mechanism for flash suppression is spatial filtering. An extension of this basic method used information from adjacent frames to estimate the flash and/or to smooth the resulting image sequence. Temporal information from adjacent frames is used as an adjunct to improve performance.


Ultrasound Based Quantitative Motion Measurement Using Speckle Size Estimation, James D. Hamilton, Larry Y. L. Mo, Gregory R. Bashford Nov 2001

Ultrasound Based Quantitative Motion Measurement Using Speckle Size Estimation, James D. Hamilton, Larry Y. L. Mo, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasound system determines the relative movement in a first direction (F1) of first matter, such as blood flow, and second matter, such as an artery wall, in a subject under study (S). A beam (B1) of ultrasound waves defining a plurality of beam positions (BP1 and BP2) and beam axes (A1 and A2) are moved in scan direction having components parallel to direction F1. First and second blocks of data representing the first and second matter, respectively, are generated. A processor (20) performs an estimation of speckle size on first data to obtain a first result, and performs analysis ...


Method And Apparatus For Adaptive Filtering By Counting Acoustic Sample Zeroes In Ultrasound Imaging, Gregory R. Bashford, Edward D. Nonnweiler, David D. Becker, David John Muzilla Oct 2000

Method And Apparatus For Adaptive Filtering By Counting Acoustic Sample Zeroes In Ultrasound Imaging, Gregory R. Bashford, Edward D. Nonnweiler, David D. Becker, David John Muzilla

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasound imaging system having an adaptive spatial filter the filter coefficients of which, for particular image parameter sample, are determined by counting the number of neighboring image parameter samples having zero or near-zero values. If the number of zero or near-zero values in a data window is greater than a predetermined threshold, the data in the window is passed, not filtered. This filter has two advantages over other spatial filters. First, image parameter data samples having only zero or near-zero neighboring values (i.e., isolated "point noise") are not smeared. Second, boundaries such as the edge of color in ...


Method And Apparatus For Controlling Acoustic Signal Bandwidth In An Ultrasonic Diagnostic Imaging System, Jeffrey R. Resnick, Gregory R. Bashford Jun 2000

Method And Apparatus For Controlling Acoustic Signal Bandwidth In An Ultrasonic Diagnostic Imaging System, Jeffrey R. Resnick, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasonic imaging system includes a receive beamformer that generates analog receive signals and a scan converter. A receive signal processing path interconnects the receive beamformer and the scan converter, and this processing path included both an A/D converter characterized by a selectable sampling rate and at least one filter characterized by at least one filter parameter. The filter parameter is selected as a function of the sampling rate to provide enhanced image quality.


Method And Apparatus For Three-Dimensional Ultrasound Imaging Of Biopsy Needle, Syed Omar Ishrak, Mir Said Seyed-Bolorforosh, William Thomas Hatfield, Todd Michael Tillman, Brian Peter Geiser, Gregory R. Bashford, Michael Joseph Washburn Apr 2000

Method And Apparatus For Three-Dimensional Ultrasound Imaging Of Biopsy Needle, Syed Omar Ishrak, Mir Said Seyed-Bolorforosh, William Thomas Hatfield, Todd Michael Tillman, Brian Peter Geiser, Gregory R. Bashford, Michael Joseph Washburn

Biomedical Imaging and Biosignal Analysis Laboratory

A method and an apparatus for three-dimensional ultrasound imaging of a needle-like instrument, such as a biopsy needle, inserted in a human body. The instrument is visualized by transmitting ultrasound beams toward the instrument and then detecting the echo signals using a linear array of transducer elements. The problem of ultrasound being reflected from a biopsy needle in a direction away from the transducer array is solved by steering the transmitted ultrasound beams t increase the angle at which the beams impinge upon the biopsy needle. Ideally the ultrasound beams are perpendicular to the needle. This increases the system's ...


Method And Apparatus For Controlling Acoustic Signal Bandwidth In An Ultrasonic Diagnostic Imaging System, Jeffrey R. Resnick, Gregory R. Bashford Nov 1999

Method And Apparatus For Controlling Acoustic Signal Bandwidth In An Ultrasonic Diagnostic Imaging System, Jeffrey R. Resnick, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An ultrasonic imaging system includes a receive beam former that generates analog receive signals and a scan converter. A receive signal processing path interconnects the receive beamformer and the scan converter, and this processing path includes both an A/D converter characterized by a selectable sampling rate and at least one filter characterized by at least one filter parameter. The filter parameter is selected as a function of the sampling rate to provide enhanced image quality.


Ultrasound Three- Dimensional Velocity Measurements By Feature Tracking, Gregory R. Bashford, Olaf T. Von Ramm May 1996

Ultrasound Three- Dimensional Velocity Measurements By Feature Tracking, Gregory R. Bashford, Olaf T. Von Ramm

Biomedical Imaging and Biosignal Analysis Laboratory

This article describes a new angle-independent method suitable for three-dimensional (3-D) blood flow velocity measurement that tracks features of the ultrasonic speckle produced by a pulse echo system. In this method, a feature is identified and followed over time to detect motion. Other blood flow velocity measurement methods typically estimate velocity using one- (1-D) or two-dimensional (2-D) spatial and time information. Speckle decorrelation due to motion in the elevation dimension may hinder this estimate of the true 3-D blood flow velocity vector. Feature tracking is a 3-D method with the ability to measure the true blood velocity vector rather than ...