Semiautomated Skeletonization of the Pulmonary Arterial Tree in Micro-CT Images

We present a simple and robust approach that utilizes planar images at different angular rotations combined with unfiltered back-projection to locate the central axes of the pulmonary arterial tree. Three-dimensional points are selected interactively by the user. The computer calculates a sub- volume unfiltered back-projection orthogonal to the vector connecting the two points and centered on the first point. Because more x-rays are absorbed at the thickest portion of the vessel, in the unfiltered back-projection, the darkest pixel is assumed to be the center of the vessel. The computer replaces this point with the newly computer-calculated point. A second back-projection is calculated around the original point orthogonal to a vector connecting the newly-calculated first point and user-determined second point. The darkest pixel within the reconstruction is determined. The computer then replaces the second point with the XYZ coordinates of the darkest pixel within this second reconstruction. Following a vector based on a moving average of previously determined 3- dimensional points along the vessel\u27s axis, the computer continues this skeletonization process until stopped by the user. The computer estimates the vessel diameter along the set of previously determined points using a method similar to the full width-half max algorithm. On all subsequent vessels, the process works the same way except that at each point, distances between the current point and all previously determined points along different vessels are determined. If the difference is less than the previously estimated diameter, the vessels are assumed to branch. This user/computer interaction continues until the vascular tree has been skeletonized

Visualization of coronary arteries in paediatric patients using whole-heart coronary magnetic resonance angiography: comparison of image-navigation and the standard approach for respiratory motion compensation

Aims: To investigate the use of respiratory motion compensation using image-based navigation (iNAV) with constant respiratory efficiency using single end-expiratory thresholding (CRUISE) for coronary magnetic resonance angiography (CMRA), and compare it to the conventional diaphragmatic navigator (dNAV) in paediatric patients with congenital or suspected heart disease. Methods: iNAV allowed direct tracking of the respiratory heart motion and was generated using balanced steady state free precession startup echoes. Respiratory gating was achieved using CRUISE with a fixed 50% efficiency. Whole-heart CMRA was acquired with 1.3mm isotropic resolution. For comparison, CMRA with identical imaging parameters were acquired using dNAV. Scan time, visualization of coronary artery origins and mid-course, imaging quality and sharpness was compared between the two sequences. Results: Forty patients (13 females; median weight: 44 kg; median age: 12.6, range: 3 months–17 years) were enrolled. 25 scans were performed in awake patients. A contrast agent was used in 22 patients. The scan time was significantly reduced using iNAV for awake patients (iNAV 7:48 ± 1:26 vs dNAV 9:48 ± 3:11, P = 0.01) but not for patients under general anaesthesia (iNAV = 6:55 ± 1:50 versus dNAV = 6:32 ± 2:16; P = 0.32). In 98% of the cases, iNAV image quality had an equal or higher score than dNAV. The visual score analysis showed a clear difference, favouring iNAV (P = 0.002). The right coronary artery and the left anterior descending vessel sharpness was significantly improved (iNAV: 56.8% ± 10.1% vs dNAV: 53.7% ± 9.9%, P < 0.002 and iNAV: 55.8% ± 8.6% vs dNAV: 53% ± 9.2%, P = 0.001, respectively). Conclusion: iNAV allows for a higher success-rate and clearer depiction of the mid-course of coronary arteries in paediatric patients. Its acquisition time is shorter in awake patients and image quality score is equal or superior to the conventional method in most cases.Medical Engineering at King’s College London WT 088641/Z/09/ZBHF Centre of Excellence RE/08/0

Serial optical coherence microscopy for label-free volumetric histopathology

The observation of histopathology using optical microscope is an essential procedure for examination of tissue biopsies or surgically excised specimens in biological and clinical laboratories. However, slide-based microscopic pathology is not suitable for visualizing the large-scale tissue and native 3D organ structure due to its sampling limitation and shallow imaging depth. Here, we demonstrate serial optical coherence microscopy (SOCM) technique that offers label-free, high-throughput, and large-volume imaging of ex vivo mouse organs. A 3D histopathology of whole mouse brain and kidney including blood vessel structure is reconstructed by deep tissue optical imaging in serial sectioning techniques. Our results demonstrate that SOCM has unique advantages as it can visualize both native 3D structures and quantitative regional volume without introduction of any contrast agents

Emerging imaging techniques in spondyloarthritis dual-energy computed tomography and new MRI sequences

Imaging of the sacroiliac joint plays a critical role in the classification of patients with axial spondyloarthritis. New imaging techniques are emerging, changing the way clinicians look at the sacroiliac joint. This article introduces the novel techniques in imaging of spondyloarthritis, including dual-energy computed tomography and new MRI sequences, with a focus on the imaging of bone marrow edema and erosions of the sacroiliac joint

MITK-ModelFit: A generic open-source framework for model fits and their exploration in medical imaging -- design, implementation and application on the example of DCE-MRI

Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and Z-spectra analysis in chemical exchange saturation transfer MRI. Most available software tools are limited to a special purpose and do not allow for own developments and extensions. Furthermore, they are mostly designed as stand-alone solutions using external frameworks and thus cannot be easily incorporated natively in the analysis workflow. We present a framework for medical image fitting tasks that is included in MITK, following a rigorous open-source, well-integrated and operating system independent policy. Software engineering-wise, the local models, the fitting infrastructure and the results representation are abstracted and thus can be easily adapted to any model fitting task on image data, independent of image modality or model. Several ready-to-use libraries for model fitting and use-cases, including fit evaluation and visualization, were implemented. Their embedding into MITK allows for easy data loading, pre- and post-processing and thus a natural inclusion of model fitting into an overarching workflow. As an example, we present a comprehensive set of plug-ins for the analysis of DCE MRI data, which we validated on existing and novel digital phantoms, yielding competitive deviations between fit and ground truth. Providing a very flexible environment, our software mainly addresses developers of medical imaging software that includes model fitting algorithms and tools. Additionally, the framework is of high interest to users in the domain of perfusion MRI, as it offers feature-rich, freely available, validated tools to perform pharmacokinetic analysis on DCE MRI data, with both interactive and automatized batch processing workflows.Comment: 31 pages, 11 figures URL: http://mitk.org/wiki/MITK-ModelFi

Improvements In computed tomography perfusion output using complex singular value decomposition and the maximum slope algorithm

OBJECTIVE: Determine if complex singular value decomposition (cSVD) used as preprocessing in the maximum slope algorithm reduces image noise of resultant physiologic parametric images. Noise will be decreased in the parametric maps of cerebral blood flow (CBF), cerebral blood volume (CBV) as compared to the same algorithm and data set with no cSVD applied. MATERIALS AND METHODS: A set of 10 patients (n=15) underwent a total combined 15 CT perfusion studies upon presenting with stroke symptoms. It was determined these patients suffered from occlusions resulting in a prolonged arrival time of blood to the brain. DICOM data files of these patients scans were selected based on this increased arrival delay. We compared the output of estimation calculations for cerebral blood flow (CBF), and cerebral blood volume (CBV), using preprocessing cSVD against the same scan data with no preprocessing cSVD. Image noise was assessed through the calculation of the standard deviation within specific regions of interest copied to specific areas of grey and white matter as well as CSF space. A decrease in the standard deviation values will indicate improvement in the noise level of the resultant images.. Results for the mean value within the regions of interest are expected to be similar between the groups calculated using cSVD and those calculated under the standard method. This will indicate the presence of minimal bias. RESULTS: Between groups of the standard processing method and the cSVD method standard deviation (SD) reductions were seen in both CBF and CBV values across all three ROIs. In grey matter measures of CBV, SD was reduced an average of 0.0034 mL/100g while measures of CBF saw SD reduced by an average of 0.073 mL/100g/min. In samples of white matter, standard deviations of CBV values were reduced on average by 0.0041mL/100g while CBF SD's were reduced by 0.073 mL/100g/min. CSF ROIs in CBV calculations saw SD reductions averaging 0.0047 mL/100g and reductions of 0.074 mL/100g/min in measures of CBF. Bias within CBV calculations was at most minimal as determined by no significant changes in mean calculated values. Calculations of CBF saw large downward bias in the mean values. CONCLUSIONS: The application of the cSVD method to preprocessing of CT perfusion imaging studies produces an effective method of noise reduction. In calculations of CBV, cSVD noise reduction results in overall improvement. In calculations of CBF, cSVD, while effective in noise reduction, caused mean values to be statistically lower than the standard method. It should be noted that there is currently no evaluation of which values can be considered more accurate physiologically. Simulations of the effect of noise on CBF showed a positive correlation suggesting that the CBF algorithm itself is sensitive to the level of noise

Three-dimensional magnetization structures revealed with X-ray vector nanotomography

In soft ferromagnetic materials, the smoothly varying magnetization leads to the formation of fundamental patterns such as domains, vortices and domain walls&lt;sup&gt;1&lt;/sup&gt;. These have been studied extensively in thin films of thicknesses up to around 200 nanometres, in which the magnetization is accessible with current transmission imaging methods that make use of electrons or soft X-rays. In thicker samples, however, in which the magnetization structure varies throughout the thickness and is intrinsically three dimensional, determining the complex magnetic structure directly still represents a challenge&lt;sup&gt;1, 3&lt;/sup&gt;. We have developed hard-X-ray vector nanotomography with which to determine the three-dimensional magnetic configuration at the nanoscale within micrometre-sized samples. We imaged the structure of the magnetization within a soft magnetic pillar of diameter 5 micrometres with a spatial resolution of 100 nanometres and, within the bulk, observed a complex magnetic configuration that consists of vortices and antivortices that form cross-tie walls and vortex walls along intersecting planes. At the intersections of these structures, magnetic singularities—Bloch points—occur. These were predicted more than fifty years ago&lt;sup&gt;4&lt;/sup&gt; but have so far not been directly observed. Here we image the three-dimensional magnetic structure in the vicinity of the Bloch points, which until now has been accessible only through micromagnetic simulations, and identify two possible magnetization configurations: a circulating magnetization structure&lt;sup&gt;5&lt;/sup&gt; and a twisted state that appears to correspond to an ‘anti-Bloch point’. Our imaging method enables the nanoscale study of topological magnetic structures&lt;sup&gt;6&lt;/sup&gt; in systems with sizes of the order of tens of micrometres. Knowledge of internal nanomagnetic textures is critical for understanding macroscopic magnetic properties and for designing bulk magnets for technological applications&lt;sup&gt;7&lt;/sup&gt;

Submillimeter diffusion tensor imaging and late gadolinium enhancement cardiovascular magnetic resonance of chronic myocardial infarction.

BackgroundKnowledge of the three-dimensional (3D) infarct structure and fiber orientation remodeling is essential for complete understanding of infarct pathophysiology and post-infarction electromechanical functioning of the heart. Accurate imaging of infarct microstructure necessitates imaging techniques that produce high image spatial resolution and high signal-to-noise ratio (SNR). The aim of this study is to provide detailed reconstruction of 3D chronic infarcts in order to characterize the infarct microstructural remodeling in porcine and human hearts.MethodsWe employed a customized diffusion tensor imaging (DTI) technique in conjunction with late gadolinium enhancement (LGE) cardiovascular magnetic resonance (CMR) on a 3T clinical scanner to image, at submillimeter resolution, myofiber orientation and scar structure in eight chronically infarcted porcine hearts ex vivo. Systematic quantification of local microstructure was performed and the chronic infarct remodeling was characterized at different levels of wall thickness and scar transmurality. Further, a human heart with myocardial infarction was imaged using the same DTI sequence.ResultsThe SNR of non-diffusion-weighted images was &gt;100 in the infarcted and control hearts. Mean diffusivity and fractional anisotropy (FA) demonstrated a 43% increase, and a 35% decrease respectively, inside the scar tissue. Despite this, the majority of the scar showed anisotropic structure with FA higher than an isotropic liquid. The analysis revealed that the primary eigenvector orientation at the infarcted wall on average followed the pattern of original fiber orientation (imbrication angle mean: 1.96 ± 11.03° vs. 0.84 ± 1.47°, p = 0.61, and inclination angle range: 111.0 ± 10.7° vs. 112.5 ± 6.8°, p = 0.61, infarcted/control wall), but at a higher transmural gradient of inclination angle that increased with scar transmurality (r = 0.36) and the inverse of wall thickness (r = 0.59). Further, the infarcted wall exhibited a significant increase in both the proportion of left-handed epicardial eigenvectors, and in the angle incoherency. The infarcted human heart demonstrated preservation of primary eigenvector orientation at the thinned region of infarct, consistent with the findings in the porcine hearts.ConclusionsThe application of high-resolution DTI and LGE-CMR revealed the detailed organization of anisotropic infarct structure at a chronic state. This information enhances our understanding of chronic post-infarction remodeling in large animal and human hearts