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ABSTRACT: When conducting optical imaging experiments, in vivo, the signal to noise ratio and effective spatial and temporal resolution is fundamentally limited by physiological motion of the tissue. A three-dimensional (3D) motion tracking scheme, using a multiphoton excitation microscope with a resonant galvanometer, (512 × 512 pixels at 33 frames s(-1)) is described to overcome physiological motion, in vivo. The use of commercially available graphical processing units permitted the rapid 3D cross-correlation of sequential volumes to detect displacements and adjust tissue position to track motions in near real-time. Motion phantom tests maintained micron resolution with displacement velocities of up to 200 μm min(-1), well within the drift observed in many biological tissues under physiologically relevant conditions. In vivo experiments on mouse skeletal muscle using the capillary vasculature with luminal dye as a displacement reference revealed an effective and robust method of tracking tissue motion to enable (1) signal averaging over time without compromising resolution, and (2) tracking of cellular regions during a physiological perturbation.
Journal of Microscopy 06/2012; 246(3):237-47. · 1.63 Impact Factor
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ABSTRACT: Diffusion-weighted MRI studies generally lose signal intensity to physiological motion, which can adversely affect quantification/diagnosis. Averaging over multiple repetitions, often used to improve image quality, does not eliminate the signal loss. In this article, PCATMIP, a combined principal component analysis and temporal maximum intensity projection approach, is developed to address this problem. Data are first acquired for a fixed number of repetitions. Assuming that physiological fluctuations of image intensities locally are likely temporally correlated unlike random noise, a local moving boxcar in the spatial domain is used to reconstruct low-noise images by considering the most relevant principal components in the temporal domain. Subsequently, a temporal maximum intensity projection yields a high signal-intensity image. Numerical and experimental studies were performed for validation and to determine optimal parameters for increasing signal intensity and minimizing noise. Subsequently, a combined principal component analysis and temporal maximum intensity projection approach was used to analyze diffusion-weighted porcine liver MRI scans. In these scans, the variability of apparent diffusion coefficient values among repeated measurements was reduced by 59% relative to averaging, and there was an increase in the signal intensity with higher intensity differences observed at higher b-values. In summary, a combined principal component analysis and temporal maximum intensity projection approach is a postprocessing approach that corrects for bulk motion-induced signal loss and improves apparent diffusion coefficient measurement reproducibility.
Magnetic Resonance in Medicine 06/2011; 65(6):1611-9. · 2.96 Impact Factor
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ABSTRACT: Free-breathing image acquisition is desirable in first-pass gadolinium-enhanced magnetic resonance imaging (MRI), but the breathing movements hinder the direct automatic analysis of the myocardial perfusion and qualitative readout by visual tracking. Nonrigid registration can be used to compensate for these movements but needs to deal with local contrast and intensity changes with time. We propose an automatic registration scheme that exploits the quasiperiodicity of free breathing to decouple movement from intensity change. First, we identify and register a subset of the images corresponding to the same phase of the breathing cycle. This registration step deals with small differences caused by movement but maintains the full range of intensity change. The remaining images are then registered to synthetic references that are created as a linear combination of images belonging to the already registered subset. Because of the quasiperiodic respiratory movement, the subset images are distributed evenly over time and, therefore, the synthetic references exhibit intensities similar to their corresponding unregistered images. Thus, this second registration step needs to account only for the movement. Validation experiments were performed on data obtained from six patients, three slices per patient, and the automatically obtained perfusion profiles were compared with profiles obtained by manually segmenting the myocardium. The results show that our automatic approach is well suited to compensate for the free-breathing movement and that it achieves a significant improvement in the average Pearson correlation coefficient between manually and automatically obtained perfusion profiles before ( 0.87 ± 0.18 ) and after ( 0.96 ± 0.09 ) registration.
IEEE Transactions on Medical Imaging 09/2010; · 3.64 Impact Factor
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01/2010: pages 235-247; , ISBN: 978-953-7619-57-2
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01/2009;
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ABSTRACT: Breathing movements during the image acquisition of first-pass gadolinium enhanced, magnetic resonance imaging (MRI) hinder a direct automatic analysis of the myocardial perfusion. In addition, a qualitative readout by visual tracking is also more difficult as well. Non-rigid registration can be used to compensate for these movements in the image series. Because of the local contrast and intensity change over time, the registration method needs to be chosen carefully. We propose to make use of the periodicity of the breathing movement when patients are allowed to breath freely during image acquisition. Specifically, we propose to first identify a subset of the images that corresponds to the same phase of the breathing cycle and register these to compensate for the residual differences. By using a combination of normalised gradient fields and the sum of squared differences we circumvent the problems arising from the change of intensity. Then, for each of the remaining images, reference images of a similar intensity distribution are created by a linear combination of images from the align subset. In the last step, registration is achieved by minimising the sum of squared differences. Our first experiments show that this approach is well suited to compensate for the breathing movements.
Computers in Cardiology, 2008; 10/2008
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ABSTRACT: Breathing movements during the image acquisition
of first-pass gadolinium enhanced, Magnetic Resonance
Imaging (MRI) hinder a direct automatic analysis of the
myocardial perfusion. In addition, a qualitative readout by
visual tracking is also more difficult as well. Non-rigid reg-
istration can be used to compensate for these movements
in the image series. Because of the local contrast and in-
tensity change over time, the registration method needs to
be chosen carefully. We propose to make use of the period-
icity of the breathing movement when patients are allowed
to breath freely during image acquisition. Specifically, we
propose to first identify a subset of the images that corre-
sponds to the same phase of the breathing cycle and reg-
ister these to compensate for the residual differences. By
using a combination of Normalised Gradient Fields and
the Sum of Squared Differences we circumvent the prob-
lems arising from the change of intensity. Then, for each
of the remaining images, reference images of a similar in-
tensity distribution are created by a linear combination of
images from the align subset. In the last step, registration
is achieved by minimising the Sum of Squared Differences.
Our first experiments show that this approach is well suited
to compensate for the breathing movements.
Proc. of the 34th Int. Conf. of Computers in Cardiology, Bologna, Italy; 01/2008
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Journal of Magn. Reson. Imag. 01/2007; 26:184-190.
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ABSTRACT: A novel spiral phase contrast technique was developed for high temporal and spatial resolution imaging of blood flow without cardiac gating. Spiral sampling of k-space has excellent flow properties and acquisition speed. Parallel imaging using the coil sensitivity maps can be used to reduce the imaging duration at the cost of SNR. An auto-calibrated spiral sensitivity encoding method is introduced and used for reconstruction of phase contrast images. Phase estimation for a simulated phantom using data from various acceleration rates was compared to the true phase map. To study the accuracy of the flow estimate with parallel image reconstruction, a high resolution cardiac gated experiment was performed and a subset of under-sampled data were reconstructed. The real-time experiments were performed to measure blood velocity in the ascending aorta and through the aortic valve with high spatial and temporal resolution. Temporal resolution of the flow images was improved by a factor of at least three with no cardiac gating signal with preserved spatial resolution. The results demonstrate the potential of using the technique for real-time flow imaging with improved spatial and temporal resolution.
Engineering in Medicine and Biology Society, 2004. IEMBS '04. 26th Annual International Conference of the IEEE; 10/2004
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ABSTRACT: A fluctuation analysis was performed on the reduced nicotine adenine dinucleotide (NADH) fluorescence signal from resting rabbit myocytes using confocal and two-photon microscopy. The purpose of this study was to establish whether any co-ordinated biochemical processes, such as binding, metabolism and inner mitochondrial membrane potential, were contributing to NADH signal fluctuations above background instrument noise. After a basic characterization of the instrument noise, time series of cellular NADH fluorescence images were collected and compared with an internal standard composed of NADH in the bathing medium. The coefficient of variation as a function of mean signal amplitude of cellular NADH fluorescence and bathing media NADH was identical even as a function of temperature. These data suggest that the fluctuations in cellular NADH fluorescence in resting myocytes are dominated by sampling noise of these instruments and not significantly modified by biological processes. Further analysis revealed no significant spatial correlations within the cell, and Fourier analysis revealed no coherent frequency information. These data suggest that the impact of biochemical processes, which might affect cellular NADH fluorescence emission, are either too small in magnitude, occurring in the wrong temporal scale or too highly spatially localized for detection using these standard optical microscopy approaches.
Journal of Microscopy 02/2004; 213(Pt 1):70-5. · 1.63 Impact Factor
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ABSTRACT: Parallel imaging applied to first-pass, contrast-enhanced cardiac MR can yield greater spatial coverage for a fixed temporal resolution. The method combines rate R=2 acceleration using TSENSE with shot-to-shot interleaving of two slices. The square root R SNR loss is largely compensated for by a longer effective repetition time (TR) and increased flip angle associated with slice interleaving. In this manner, increased spatial coverage is achieved while comparable or better image quality is maintained. Single-heartbeat temporal resolution was accomplished with spatial coverage of eight slices at heart rates up to 71 bpm, six slices up to 95 bpm, and four slices up to 143 bpm. Experiments in normal subjects (N=6) were performed to assess signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) values.
Magnetic Resonance in Medicine 02/2004; 51(1):200-4. · 2.96 Impact Factor
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ABSTRACT: Parallel imaging applied to first-pass, contrast-enhanced cardiac MR can yield greater spatial coverage for a fixed temporal resolution. The method combines rate R = 2 acceleration using TSENSE with shot-to-shot interleaving of two slices. The √R SNR loss is largely compensated for by a longer effective repetition time (TR) and increased flip angle associated with slice interleaving. In this manner, increased spatial coverage is achieved while comparable or better image quality is maintained. Single-heartbeat temporal resolution was accomplished with spatial coverage of eight slices at heart rates up to 71 bpm, six slices up to 95 bpm, and four slices up to 143 bpm. Experiments in normal subjects (N = 6) were performed to assess signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) values. Magn Reson Med 51:200–204, 2004. Published 2003 Wiley-Liss, Inc.
Magnetic Resonance in Medicine 12/2003; 51(1):200 - 204. · 2.96 Impact Factor
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ABSTRACT: The sensitivity encoding (SENSE) method of parallel MR accelerated imaging is evaluated and compared for 1-d and 2-d surface coil array geometries. Accelerated MR imaging using SENSE may be applied to volume imaging using either 3-d or 2-d multi-slice acquisition strategies. For higher accelerations such as rate R=4, 3-d SENSE may be applied along either or both phase encode directions. Image quality (SENSE g-factor) is compared for R=4 acceleration implemented with a reduced number of phase encodes in the y-direction, and (assuming a 3-d acquisition) with a reduced number of phase encodes in both yand z-directions. Simulations show that the performance for 1-d and 2-d array geometries depends highly on the slice orientation.
Biomedical Imaging, 2002. Proceedings. 2002 IEEE International Symposium on; 02/2002
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ABSTRACT: In this article, a method for phased array combining is formulated which may be used to cancel ghosts caused by a variety of distortion mechanisms, including space variant distortions such as local flow or off-resonance. This method is based on a constrained optimization, which optimizes SNR subject to the constraint of nulling ghost artifacts at known locations. The resultant technique is similar to the method known as sensitivity encoding (SENSE) used for accelerated imaging; however, in this formulation it is applied to full field-of-view (FOV) images. The method is applied to multishot EPI with noninterleaved phase encode acquisition. A number of benefits, as compared to the conventional interleaved approach, are reduced distortion due to off-resonance, in-plane flow, and EPI delay misalignment, as well as eliminating the need for echo-shifting. Experimental results demonstrate the cancellation for both phantom as well as cardiac imaging examples.
Magnetic Resonance in Medicine 09/2001; 46(2):335-43. · 2.96 Impact Factor
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ABSTRACT: A number of different methods have been demonstrated which increase the speed of MR acquisition by decreasing the number of sequential phase encodes. The UNFOLD technique is based on time interleaving of k-space lines in sequential images and exploits the property that the outer portion of the field-of-view is relatively static. The differences in spatial sensitivity of multiple receiver coils may be exploited using SENSE or SMASH techniques to eliminate the aliased component that results from undersampling k-space. In this article, an adaptive method of sensitivity encoding is presented which incorporates both spatial and temporal filtering. Temporal filtering and spatial encoding may be combined by acquiring phase encodes in an interleaved manner. In this way the aliased components are alternating phase. The SENSE formulation is not altered by the phase of the alias artifact; however, for imperfect estimates of coil sensitivities the residual artifact will have alternating phase using this approach. This is the essence of combining temporal filtering (UNFOLD) with spatial sensitivity encoding (SENSE). Any residual artifact will be temporally frequency-shifted to the band edge and thus may be further suppressed by temporal low-pass filtering. By combining both temporal and spatial filtering a high degree of alias artifact rejection may be achieved with less stringent requirements on accuracy of coil sensitivity estimates and temporal low-pass filter selectivity than would be required using each method individually. Experimental results that demonstrate the adaptive spatiotemporal filtering method (adaptive TSENSE) with acceleration factor R = 2, for real-time nonbreath-held cardiac MR imaging during exercise induced stress are presented.
Magnetic Resonance in Medicine 06/2001; 45(5):846-52. · 2.96 Impact Factor
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ABSTRACT: To improve real-time control of interventional procedures such as guidance of catheters, monitoring of ablation therapy, or control of dosage during drug delivery, the image acquisition and reconstruction must be high speed and have low latency (small time delay) in processing. A number of different methods have been demonstrated which increase the speed of MR acquisition by decreasing the number of sequential phase-encodes. A design and implementation of the UNFOLD method which achieves the desired low latency with a recursive temporal filter is presented. The recursive filter design is characterized for this application and compared with more commonly used moving average filters. Experimental results demonstrate low-latency UNFOLD for two applications: 1) high-speed, real-time imaging of the heart to be used in conjunction with cardiac interventional procedures; and 2) the injection of drugs into muscle tissue with contrast enhancement, i.e., monitoring needle insertion and injection of a drug with contrast enhancement properties. Proof-of-concept was demonstrated by injecting a contrast agent. In both applications the UNFOLD technique was used to double the frame rate.
Magnetic Resonance in Medicine 01/2001; 44(6):933-9. · 2.96 Impact Factor
