David W. Holdsworth

Micro-CT in small animal and specimen imaging

Abstract Laboratory systems for microscopic computed tomography (micro-CT) have recently evolved from specialized prototype tools to become essential components of many research laboratories. The availability of commercial systems with almost microscopic resolution and the capability to image live animals has opened up entirely new applications for micro-CT in laboratory investigation. This review describes the technical aspects of micro-CT and highlights some current research applications. Micro-CT has the potential to replace serial histology as the reference standard in many in vitro studies, and provides a practical approach to obtain quantitative information during some longitudinal investigations in vivo .

Characterization of common carotid artery blood-flow waveforms in normal human subjects

Knowledge of human blood-flow waveforms is required for in vitro investigations and numerical modelling. Parameters of interest include: velocity and flow waveform shapes, inter- and intra-subject variability and frequency content. We characterized the blood-velocity waveforms in the left and right common carotid arteries (CCAs) of 17 normal volunteers (24 to 34 years), analysing 3560 cardiac cycles in total. Instantaneous peak-velocity (Vpeak) measurements were obtained using pulsed-Doppler ultrasound with simultaneous collection of ECG data. An archetypal Vpeak waveform was created using velocity and timing parameters at waveform feature points. We report the following timing (post-R-wave) and peak-velocity parameters: cardiac interbeat interval (T(RR)) = 0.917 s (intra-subject standard deviation = +/- 0.045 s); cycle-averaged peak-velocity (V(CYC)) = 38.8 cm s(-1) (+/-1.5 cm s(-1)); maximum systolic Vpeak = 108.2 cm s(-1) (+/-3.8 cm s(-1)) at 0.152 s (+/-0.008 s); dicrotic notch Vpeak = 19.4 cm s(-1) (+/-2.9 cm s(-1)) at 0.398 s (+/-0.007 s). Frequency components below 12 Hz constituted 95% of the amplitude spectrum. Flow waveforms were computed from Vpeak by analytical solution of Womersley flow conditions (derived mean flow = 6.0 ml s(-1)). We propose that realistic, pseudo-random flow waveform sequences can be generated for experimental studies by varying, from cycle to cycle, only T(RR) and V(CYC) of a single archetypal waveform.

Characterization of volumetric flow rate waveforms in the normal internal carotid and vertebral arteries

Knowledge of normal cerebrovascular volumetric flow rate (VFR) dynamics is of interest for establishing baselines, and for providing input data to cerebrovascular model studies. Retrospectively gated phase contrast magnetic resonance imaging was used to measure time-resolved VFR waveforms from the two internal carotid arteries (ICA) and two vertebral arteries (VA) of 17 young, normal volunteers (16M:1F) at rest in a supine posture. After normalizing each waveform to its respective cycle-averaged VFR, the timing and amplitude of feature points from the individual waveforms were averaged together to produce archetypal ICA and VA waveform shapes. Despite significant inter-individual differences in cycle-averaged VFR within the ICA compared to VA (275+/-52 versus 91+/-18 mL min-1), the respective waveform shapes were qualitatively similar overall. The VA waveform shape did, however, exhibit significantly higher amplitudes (e.g., peak:average VFR of 1.78+/-0.30 versus 1.66+/-0.16; p<0.05) and significantly higher variability both between and within subjects. A significant correlation was observed between peak and cycle-averaged VFR, suggesting that the representative waveform shapes presented here-when scaled by an individuals cycle-averaged VFR-may be used to characterize normal ICA and VA flow rate dynamics. This capability may be of particular utility for studies where cerebrovascular flow dynamics are required, but only average flow rates are available.

In Vivo Small Animal Imaging using Micro-CT and Digital Subtraction Angiography

Small-animal imaging has a critical role in phenotyping, drug discovery and in providing a basic understanding of mechanisms of disease. Translating imaging methods from humans to small animals is not an easy task. The purpose of this work is to review in vivo x-ray based small-animal imaging, with a focus on in vivo micro-computed tomography (micro-CT) and digital subtraction angiography (DSA). We present the principles, technologies, image quality parameters and types of applications. We show that both methods can be used not only to provide morphological, but also functional information, such as cardiac function estimation or perfusion. Compared to other modalities, x-ray based imaging is usually regarded as being able to provide higher throughput at lower cost and adequate resolution. The limitations are usually associated with the relatively poor contrast mechanisms and potential radiation damage due to ionizing radiation, although the use of contrast agents and careful design of studies can address these limitations. We hope that the information will effectively address how x-ray based imaging can be exploited for successful in vivo preclinical imaging.

Fundamental image quality limits for microcomputed tomography in small animals

Small-animal imaging has become increasingly more important as transgenic and knockout mice are produced to model human diseases. One imaging technique that has emerged is microcomputed tomography (micro-CT). For live-animal imaging, the precision in the images will be determined by the x-ray dose given to the animal. As a result, we propose a simple method to predict the noise performance of an x-ray micro-CT system as a function of dose and image resolution. An ideal, quantum-noise limited micro-CT scanner, assumed to have perfect resolution and ideal efficiency, was modeled. Using a simplified model, the coefficient of variation (COV) of the linear attenuation coefficient was calculated for a range of entrance doses and isotropic voxel sizes. COV calculations were performed for the ideal case and with simulated imperfections in efficiency and resolution. Our model was validated in phantom studies and mouse images were acquired with a specimen scanner to illustrate the results. A simplified model of noise propagation in the case of isotropic resolution indicates that the COV in the linear attenuation coefficient is proportional to (dose)(-1/2) and to the (isotropic voxel size)(-2) in the reconstructed volume. Therefore an improvement in the precision can be achieved only by increasing the isotropic voxel size (thereby decreasing the resolution of the image) or by increasing the x-ray dose. For the ideal scanner, a COV of 1% in the linear attenuation coefficient for an image of a mouse exposed to 0.25 Gy is obtained with a minimum isotropic voxel size of 135 microm. However, the same COV is achieved at a dose of 5.0 Gy with a 65 microm isotropic voxel size. Conversely, for a 68 mm diameter rat, a COV of 1% obtained from an image at 5.0 Gy would require an isotropic voxel size of 100 microm. These results indicate that short-term, potentially lethal, effects of ionizing radiation will limit high-resolution live animal imaging. As improvements in detector technology allow the resolution to improve, by decreasing the detector element size to tens of microns or less, high quality images will be limited by the x-ray dose administered. For the highest quality images, these doses will approach the lethal dose or LD50 for the animals. Approaching the lethal dose will affect the way experiments are planned, and may reduce opportunities for experiments involving imaging the same animal over time. Dose considerations will become much more important for live small-animal imaging as the limits of resolution are tested.

Computer controlled positive displacement pump for physiological flow simulation

A computer-controlled pump for use both in the study of vascular haemodynamics and in the calibration of clinical devices which measure blood flow is designed. The novel design of this pump incorporates two rack-mounted pistons, driven into opposing cylinders by a micro-stepping motor. This approach allows the production of nearly uninterrupted steady flow, as well as a variety of pulsatile wave-forms, including waveforms with reverse flow. The capabilities of this pump to produce steady flow from 0·1 to 60 mls−1, as well as sinusoidal flow and physiological flow, such as that found in the common femoral and common carotid arteries are demonstrated. Cycle-to-cycle reproducibility is very good, with an average variation of 0·1 mls−1 over thousands of cycles.

Accuracy of Computational Hemodynamics in Complex Arterial Geometries Reconstructed from Magnetic Resonance Imaging

AbstractPurpose: Combining computational blood flow modeling with three-dimensional medical imaging provides a new approach for studying links between hemodynamic factors and arterial disease. Although this provides patient-specific hemodynamic information, it is subject to several potential errors. This study quantifies some of these errors and identifies optimal reconstruction methodologies. Methods: A carotid artery bifurcation phantom of known geometry was imaged using a commercial magnetic resonance (MR) imager. Three-dimensional models were reconstructed from the images using several reconstruction techniques, and steady and unsteady blood flow simulations were performed. The carotid bifurcation from a healthy, human volunteer was then imaged in vivo, and geometric models were reconstructed. Results: Reconstructed models of the phantom showed good agreement with the gold standard geometry, with a mean error of approximately 15% between the computed wall shear stress fields. Reconstructed models of the in vivo carotid bifurcation were unacceptably noisy, unless lumenal profile smoothing and approximating surface splines were used. Conclusions: All reconstruction methods gave acceptable results for the phantom model, but in vivo models appear to require smoothing. If proper attention is paid to smoothing and geometric fidelity issues, models reconstructed from MR images appear to be suitable for use in computational studies of in vivo hemodynamics.

PIV-Measured Versus CFD-Predicted Flow Dynamics in Anatomically Realistic Cerebral Aneurysm Models

Computational fluid dynamics (CFD) modeling of nominally patient-specific cerebral aneurysms is increasingly being used as a research tool to further understand the development, prognosis, and treatment of brain aneurysms. We have previously developed virtual angiography to indirectly validate CFD-predicted gross flow dynamics against the routinely acquired digital subtraction angiograms. Toward a more direct validation, here we compare detailed, CFD-predicted velocity fields against those measured using particle imaging velocimetry (PIV). Two anatomically realistic flow-through phantoms, one a giant internal carotid artery (ICA) aneurysm and the other a basilar artery (BA) tip aneurysm, were constructed of a clear silicone elastomer. The phantoms were placed within a computer-controlled flow loop, programed with representative flow rate waveforms. PIV images were collected on several anterior-posterior (AP) and lateral (LAT) planes. CFD simulations were then carried out using a well-validated, in-house solver, based on micro-CT reconstructions of the geometries of the flow-through phantoms and inlet/outlet boundary conditions derived from flow rates measured during the PIV experiments. PIV and CFD results from the central AP plane of the ICA aneurysm showed a large stable vortex throughout the cardiac cycle. Complex vortex dynamics, captured by PIV and CFD, persisted throughout the cardiac cycle on the central LAT plane. Velocity vector fields showed good overall agreement. For the BA, aneurysm agreement was more compelling, with both PIV and CFD similarly resolving the dynamics of counter-rotating vortices on both AP and LAT planes. Despite the imposition of periodic flow boundary conditions for the CFD simulations, cycle-to-cycle fluctuations were evident in the BA aneurysm simulations, which agreed well, in terms of both amplitudes and spatial distributions, with cycle-to-cycle fluctuations measured by PIV in the same geometry. The overall good agreement between PIV and CFD suggests that CFD can reliably predict the details of the intra-aneurysmal flow dynamics observed in anatomically realistic in vitro models. Nevertheless, given the various modeling assumptions, this does not prove that they are mimicking the actual in vivo hemodynamics, and so validations against in vivo data are encouraged whenever possible.

Three-dimensional computed tomographic reconstruction using a C-arm mounted XRII: correction of image intensifier distortion.

X-ray image intensifiers (XRIIs) have many applications in diagnostic imaging including acquisition of near-real-time projection images of the intracranial and coronary vasculature. Recently, there has been some interest in using this projection data to generate three-dimensional (3-D) computed tomographic (CT) reconstructions. The XRII and x-ray tube are rotated around the object, acquiring sufficient data for the simultaneous reconstruction of many transverse slices. Three-dimensional reconstructions are compromised, however, if the projection data is geometrically distorted in any way. Previous studies have shown the distortion in XRIIs to be substantial and to be highly angular dependent. In this paper, we present a global correction technique which provides a table of correction coefficients for an image acquired at any arbitrary angle about the patient. The coefficients are generated using a linear least-squares fit between the detected and known locations of a grid of small steel beads which is attached to the XRII (27 cm nominal diameter). We have performed corrections on 100 images obtained during rotation of the gantry through 200 degrees and find that a fifth-order polynomial provides optimum image distortion reduction (mean residual distortion of 0.07 pixels), however, fourth-order polynomials provide sufficient distortion reduction for our application (mean residual displacement of 0.1 pixels). Using sixth-order polynomials does not provide a statistically significant reduction in image distortion. The spatial distribution of residual distortion did not demonstrate any particular pattern over the face of the XRII. Image angle and coefficient angle must be known to within +/- 2 degrees in order to keep the mean residual distortion be approximately 0.5 pixels.

A quality assurance phantom for the performance evaluation of volumetric micro-CT systems.

Small-animal imaging has recently become an area of increased interest because more human diseases can be modeled in transgenic and knockout rodents. As a result, micro-computed tomography (micro-CT) systems are becoming more common in research laboratories, due to their ability to achieve spatial resolution as high as 10 microm, giving highly detailed anatomical information. Most recently, a volumetric cone-beam micro-CT system using a flat-panel detector (eXplore Ultra, GE Healthcare, London, ON) has been developed that combines the high resolution of micro-CT and the fast scanning speed of clinical CT, so that dynamic perfusion imaging can be performed in mice and rats, providing functional physiological information in addition to anatomical information. This and other commercially available micro-CT systems all promise to deliver precise and accurate high-resolution measurements in small animals. However, no comprehensive quality assurance phantom has been developed to evaluate the performance of these micro-CT systems on a routine basis. We have designed and fabricated a single comprehensive device for the purpose of performance evaluation of micro-CT systems. This quality assurance phantom was applied to assess multiple image-quality parameters of a current flat-panel cone-beam micro-CT system accurately and quantitatively, in terms of spatial resolution, geometric accuracy, CT number accuracy, linearity, noise and image uniformity. Our investigations show that 3D images can be obtained with a limiting spatial resolution of 2.5 mm(-1) and noise of +/-35 HU, using an acquisition interval of 8 s at an entrance dose of 6.4 cGy.