Marek Karolczak

Implementation of a cone-beam reconstruction algorithm for the single-circle source orbit with embedded misalignment correction using homogeneous coordinates.

We present an efficient implementation of an approximate cone-beam image reconstruction algorithm for application in tomography, which accounts for scanner mechanical misalignment. The implementation is based on the algorithm proposed by Feldkamp et al. and is directed at circular scan paths. The algorithm has been developed for the purpose of reconstructing volume data from projections acquired in an experimental x-ray micro-tomography (microCT) scanner. To mathematically model misalignment we use matrix notation with homogeneous coordinates to describe the scanner geometry, its misalignment, and the acquisition process. For convenience analysis is carried out for x-ray CT scanners, but it is applicable to any tomographic modality, where two-dimensional projection acquisition in cone beam geometry takes place, e.g., single photon emission computerized tomography. We derive an algorithm assuming misalignment errors to be small enough to weight and filter original projections and to embed compensation for misalignment in the backprojection. We verify the algorithm on simulations of virtual phantoms and scans of a physical multidisk (Defrise) phantom.

Mikro-CT : Technologie und Applikationen zur Erfassung von Knochenarchitektur

ZusammenfassungDie Stärke und Bruchfestigkeit von Knochen wird durch seine trabekuläre und kortikale Struktur bestimmt. Mit zweidimensionalen Meßverfahren wie der Histomorphometrie kann die dreidimensionale Natur des Trabekelnetzwerkes nicht adäquat erfaßt werden. Isotrope 3D Datensätze können mit dem neuen bildgebenden Verfahren der µCT erzeugt werden. Die Frage nach geeigneten Strukturparametern zur Beschreibung des trabekulären Netzwerkes ist allerdings letztendlich noch nicht gelöst. In diesem Beitrag beschreiben wir Technologie und Anwendungen der µCT, welche für das Gebiet der Osteologie relevant sind. Als wichtigste technische Faktoren in diesem Kontext sind derzeit zu nennen: 1. Eine räumliche Auflösung von 5–10 µm kann erzielt werden. 2. Probengröße und Auflösung hängen ca. über einen Faktor 1000 zusammen: Bei einer zu erzielenden Auflösung von 10 µm ist die maximale Probengröße auf etwa 1 cm begrenzt. 3. Die Scanzeiten liegen im Bereich von Minuten bis Stunden. Im Bereich der Osteologie wird die µCT derzeit auf 5 Gebieten eingesetzt: 1. Zur Suche und Optimierung von Parametern, die die dreidimensionale Trabekelstruktur charakterisieren. 2. Die Anwendung von Finite-Elemente Methoden zur Bestimmung der biomechanischen Wertigkeit der stereologischen Parameter. 3. Der Einsatz in der präklinischen Forschung zu in-vivo Verlaufskontrollen in kleinen Labortieren. 4. Die Validierung von Analysemethoden, die in hochauflösenden in-vivo Verfahren zur Osteoporosediagnostik angewendet werden. 5. Die dreidimensionale Quantifizierung von Modeling- und Remodelingprozessen.SummaryThe strength and fracture resistance of bone is determined by the structure of the trabecular network and the cortical shell. While standard 2D techniques like histomorphometry are inadequate to assess the 3D nature of the trabecular network, isotropic 3D datasets of this network can be acquired with the new imaging modality of µCT. However, so far the quantitative analysis of the generated datasets, in particular the extraction of appropriate parameters describing the bone structure, has not been finally solved. In this article we describe the technology and applications of µCT systems relevant in the field of osteology. The most important technical features of current µCT systems in this context are: 1. A spatial resolution down to 5–10 µm can be achieved. 2. The maximum sample size is related to the desired resolution by a factor of approximately 1000, that is, a resolution of 10 µm limits the maximum sample size to approximately 1 cm. 3. Scan times for µCT systems vary between minutes and hours.Currently five areas for the application of µCT systems in osteology can be identified: 1. The search of parameters characterizing the 3D trabecular structure. 2. The application of finite element models to determine the biochemical competence of the structural parameters. 3. The use of µCT in preclinical trials to study drug effects in small animals. 4. The validation of analysis methods used in high-resolution in-vivo imaging systems. 5. The 3D quantification of modeling and remodeling processes.

Angiofil-mediated visualization of the vascular system by microcomputed tomography: a feasibility study

Visualization of the vascular systems of organs or of small animals is important for an assessment of basic physiological conditions, especially in studies that involve genetically manipulated mice. For a detailed morphological analysis of the vascular tree, it is necessary to demonstrate the system in its entirety. In this study, we present a new lipophilic contrast agent, Angiofil®, for performing postmortem microangiography by using microcomputed tomography. The new contrast agent was tested in 10 wild‐type mice. Imaging of the vascular system revealed vessels down to the caliber of capillaries, and the digital three‐dimensional data obtained from the scans allowed for virtual cutting, amplification, and scaling without destroying the sample. By use of computer software, parameters such as vessel length and caliber could be quantified and remapped by color coding onto the surface of the vascular system. The liquid Angiofil® is easy to handle and highly radio‐opaque. Because of its lipophilic abilities, it is retained intravascularly, hence it facilitates virtual vessel segmentation, and yields an enduring signal which is advantageous during repetitive investigations, or if samples need to be transported from the site of preparation to the place of actual analysis, respectively. These characteristics make Angiofil® a promising novel contrast agent; when combined with microcomputed tomography, it has the potential to turn into a powerful method for rapid vascular phenotyping. Microsc. Res. Tech., 2008.

In vivo micro-CT imaging of rat brain glioma: A comparison with 3 T MRI and histology

The aim of this study was to evaluate the potential of a novel micro-CT system to image in vivo the extent of tumor in a rat model of malignant glioma compared to 3T magnetic resonance imaging (MRI) and histology. Fourteen animals underwent double dose contrast-enhanced imaging with micro-CT and 3T MRI using a clinical machine at day 10 after stereotactic F98 glioma cell implantation. Calculation of the volume of the contrast-uptaking part of the tumor was done by manually outlining the tumor contours by two experienced neuroradiologists. The micro-CT- and MRI-derived tumor volumes were compared to histology as gold standard (hematoxylin and eosin staining and fluorescence staining). There was high interobserver reability regarding the tumor volumes (Crombachs alpha>0.81). Also, there was good correlation of micro-CT- and high-field MRI-derived tumor volumes compared to histology: 72+/-21 mm3 and 69+/-23 mm3 compared to 81+/-14 mm3, respectively (r>0.76). Both the micro-CT- and MRI-derived tumor volumes were not significantly smaller compared to histology (P>0.14). In conclusion, micro-CT allows in vivo imaging of the contrast-enhancing part of experimental gliomas with an accuracy comparable to high-field MRI.

A new weighting function to achieve high temporal resolution in circular cone-beam CT with shifted detectors.

The size of the field of measurement (FOM) in computed tomography is limited by the size of the x-ray detector. In general, the detector is mounted symmetrically with respect to the rotation axis such that the transaxial FOM diameter approximately equals the lateral dimensions of the detector when being demagnified to the isocenter. To enlarge the FOM one may laterally shift the detector by up to 50% of its size. Well-known weighting functions must then be applied to the raw data prior to convolution and backprojection. In this case, a full scan or a scan with more than 360° angular coverage is required to obtain complete data. However, there is a small region, the inner FOM, that is covered redundantly and where a partial scan reconstruction may be sufficient. A new weighting function is proposed that allows one to reconstruct partial scans in that inner FOM while it reconstructs full scan or overscan data for the outer FOM, which is the part that contains no redundancies. The presented shifted detector partial scan algorithm achieves a high temporal resolution in the inner FOM while maintaining truncation-free images for the outer part. The partial scan window can be arbitrarily shifted in the angular direction, what corresponds to shifting the temporal window of the data shown in the inner FOM. This feature allows for the reconstruction of dynamic CT data with high temporal resolution. The approach presented here is evaluated using simulated and measured data for a dual source micro-CT scanner with rotating gantry.

Assessment of spatial resolution in CT

To quantify spatial resolution in CT one typically performs separate measurements for the lateral and the longitudinal point spread function (PSF). Many procedures further require reconstructions with very small voxel sizes, e.g. when wire phantoms are scanned. This, however, may already change the shape of the PSF. For example, this is the case when Moiré filters are applied or when iterative image reconstruction algorithms are used. Aiming at assessing the point spread function (PSF) and the modulation transfer function (MTF) of a CT scanner using a single measurement we propose to measure a sphere, perform a standard image reconstruction and evaluate profiles through the sphere surface. The radial symmetry of CT scanners allows to reduce the dimensionality of the PSF and the MTF from three to two by radial averaging. It is shown that the resulting two-dimensional profiles can be decomposed into a radial and into a longitudinal component by two-dimensional parallel-beam filtered backprojection. Our method was assessed using simulated and measured data of a homogeneous sphere. The measurements were performed with the capable in-vivo cone-beam micro-CT scanner VAMP TomoScope 30s. The longitudinal and radial PSFs, and the corresponding MTFs, highly agree with those obtained with conventional methods, for both the simulations and the measurements. Figures of merit extracted from the curves, such as the full width at half maximum of the PSF or the 10% value of the MTF, differ by less than 5% between the new method and the conventional approaches. Therewith it gives a technique which requires only one, easy to handle, measurement of a sphere to calculate radial and longitudinal PSF and therefrom obtain the corresponding MTFs. Furthermore it does not require a dedicated reconstruction with very small voxels. Therefore it appears superior to existing methods.

X-Ray and X-Ray-CT

Since their discovery in 1895, X-rays have been widely used for imaging humans. Recently, they have also gained an importance in small animal imaging (SAI). Most techniques known from clinical medicine, including single- and dual-energy X-ray imaging, have been successfully ported to SAI and are the subject of this chapter. As trivial as it is, simple X-ray examinations may bring diagnostically valuable information in a variety of applications. Unenhanced radiography reveals skeletal anatomy, contrast-enhanced imaging allows improved visualization of the vasculature and strongly vascularized areas, and dedicated methods such as bone densitometry deliver quantitative information. In analogy to clinical X-ray imaging, we will separately describe standard two-dimensional (2D) projection imaging and the more advanced three-dimensional (3D) computed tomography (CT) imaging techniques. Also in analogy to clinical applications, CT is considered to be of significantly higher importance as it provides more information and possibilities than conventional 2D approaches. It will therefore be covered in much more detail.

Comparative investigation of the detective quantum efficiency of direct and indirect conversion detector technologies in dedicated breast CT.

PURPOSE To investigate the dose saving potential of direct-converting CdTe photon-counting detector technology for dedicated breast CT. MATERIALS AND METHODS We analyzed the modulation transfer function (MTF), the noise power spectrum (NPS) and the detective quantum efficiency (DQE) of two detector technologies, suitable for breast CT (BCT): a flat-panel energy-integrating detector with a 70 μm and a 208 μm thick gadolinium oxysulfide (GOS) and a 150 μm thick cesium iodide (CsI) scintillator and a photon-counting detector with a 1000 μm thick CdTe sensor. RESULTS The measurements for GOS scintillator thicknesses of 70 μm and 208 μm delivered 10% pre-sampled MTF values of 6.6 mm(-1) and 3.2 mm(-1), and DQE(0) values of 23% and 61%. The 10% pre-sampled MTF value for the 150 μm thick CsI scintillator 6.9 mm(-1), and the DQE(0) value was 49%. The CdTe sensor reached a 10% pre-sampled MTF value of 8.5 mm(-1) and a DQE(0) value of 85%. CONCLUSION The photon-counting CdTe detector technology allows for significant dose reduction compared to the energy-integrating scintillation detector technology used in BCT today. Our comparative evaluation indicates that a high potential dose saving may be possible for BCT by using CdTe detectors, without loss of spatial resolution.

Bar and Point Test Patterns Generated by Dry-Etching for Measurement of High Spatial Resolution in Micro-CT

The purpose of this work was to evaluate a novel method for manufacturing test patterns with high spatial resolution to be used for visual inspection of spatial resolution of micro-CT systems. High resolution test patterns of less than 50 μm line widths or point diameter for inspection of the performance of a micro-CT system have not been reported before. Test patterns were created on a silicon wafer using a dry etching method. For reference spatial resolution measurements were carried out on micro-CT systems using thin tungsten wires. The modulation transfer function (MTF) subsequently derived from a point spread function (PSF) of the wire profile was measured to determine spatial resolution at 10% of the contrast ratio. The test pattern chip was scanned under the same conditions for visual inspection of the spatial resolution. The results of the wire-based MTF calculations and visual inspection of the test patterns were found in very good agreement. In the manufacturing process some limitations were found due to over-etching and maximum etch depth for smaller patterns (5 μm) adjacent to larger structures (150 μm) on one chip. Nevertheless, these circumstances can be solved by using choice of pattern sizes for specific scanner setup. The novel method of creating high resolution test patterns for quick visual inspection offers a very attractive solution, but also allows for quantitative evaluation.

Effects of defect pixel correction algorithms for x-ray detectors on image quality in planar projection and volumetric CT data sets

In this study we compared various defect pixel correction methods for reducing artifact appearance within projection images used for computed tomography (CT) reconstructions.Defect pixel correction algorithms were examined with respect to their artifact behaviour within planar projection images as well as in volumetric CT reconstructions. We investigated four algorithms: nearest neighbour, linear and adaptive linear interpolation, and a frequency-selective spectral-domain approach.To characterise the quality of each algorithm in planar image data, we inserted line defects of varying widths and orientations into images. The structure preservation of each algorithm was analysed by corrupting and correcting the image of a slit phantom pattern and by evaluating its line spread function (LSF). The noise preservation was assessed by interpolating corrupted flat images and estimating the noise power spectrum (NPS) of the interpolated region.For the volumetric investigations, we examined the structure and noise preservation within a structured aluminium foam, a mid-contrast cone-beam phantom and a homogeneous Polyurethane (PUR) cylinder.The frequency-selective algorithm showed the best structure and noise preservation for planar data of the correction methods tested. For volumetric data it still showed the best noise preservation, whereas the structure preservation was outperformed by the linear interpolation.The frequency-selective spectral-domain approach in the correction of line defects is recommended for planar image data, but its abilities within high-contrast volumes are restricted. In that case, the application of a simple linear interpolation might be the better choice to correct line defects within projection images used for CT.