Characterizing the parallax error in multi-pinhole micro-SPECT reconstruction

The usage of pinholes is very important in preclinical micro-SPECT. Pinholes can magnify the object onto the detector, resulting in better system resolutions than the detector resolution. The loss in sensitivity is usually countered by adding more pinholes, each projecting onto a specific part of the detector. As a result, gamma rays have an oblique incidence to the detector. This causes displacement and increased uncertainty in the position of the interaction of the gamma ray in the detector, also known as parallax errors or depth-of-interaction (DOI) errors. This in turn has a large influence on image reconstruction algorithms using ray tracers as a forward projector model, as the end-point of each ray on the detector has to be accurately known. In this work, we used GATE to simulate the FLEX Triumph-I system (Gamma Medica-Ideas, Northridge, CA), a CZT-based multi-pinhole micro-SPECT system. This system uses 5 mm thick CZT pixels, with 1.5 mm pixel pitch. The simulated information was then used to enhance the image resolution by accurately modeling the DOI. Two hundred point sources were simulated and rebinned to use the DOI information. This data was then used in a GPU-based iterative reconstruction algorithm taking the simulated DOI into account. The average displacement was then determined for all point sources, and the FWHM was calculated in three dimensions, by fitting the point sources with 3D Gaussians. We show that the displacement is reduced by 83% on average. We also show a 15% resolution gain when only 5 DOI levels are used

Iterative CT reconstruction using shearlet-based regularization

In computerized tomography, it is important to reduce the image noise without increasing the acquisition dose. Extensive research has been done into total variation minimization for image denoising and sparse-view reconstruction. However, TV minimization methods show superior denoising performance for simple images (with little texture), but result in texture information loss when applied to more complex images. Since in medical imaging, we are often confronted with textured images, it might not be beneficial to use TV. Our objective is to find a regularization term outperforming TV for sparse-view reconstruction and image denoising in general. A recent efficient solver was developed for convex problems, based on a split-Bregman approach, able to incorporate regularization terms different from TV. In this work, a proof-of-concept study demonstrates the usage of the discrete shearlet transform as a sparsifying transform within this solver for CT reconstructions. In particular, the regularization term is the 1-norm of the shearlet coefficients. We compared our newly developed shearlet approach to traditional TV on both sparse-view and on low-count simulated and measured preclinical data. Shearlet-based regularization does not outperform TV-based regularization for all datasets. Reconstructed images exhibit small aliasing artifacts in sparse-view reconstruction problems, but show no staircasing effect. This results in a slightly higher resolution than with TV-based regularization

Improved treebank querying: a facelift for GrETEL

We describe the improvements to the interface of GrETEL, an online tool for querying treebanks. We demonstrate how we employed the results of two usability tests and individual user feedback in order to create a more user-friendly interface which meets the users’ needs

Replacing vascular corrosion casting by in-vivo micro-CT imaging for building 3D cardiovascular models in mice

The purpose of this study was to investigate if in vivo micro-computed tomography (CT) is a reliable alternative to micro-CT scanning of a vascular corrosion cast. This would allow one to study the early development of cardiovascular diseases. Datasets using both modalities were acquired, segmented, and used to generate a 3D geometrical model from nine mice. As blood pool contrast agent, Fenestra VC-131 was used. Batson's No. 17 was used as casting agent. Computational fluid dynamics simulations were performed on both datasets to quantify the difference in wall shear stress (WSS). Aortic arch diameters show 30% to 40% difference between the Fenestra VC-131 and the casted dataset. The aortic arch bifurcation angles show less than 20% difference between both datasets. Numerically computed WSS showed a 28% difference between both datasets. Our results indicate that in vivo micro-CT imaging can provide an excellent alternative for vascular corrosion casting. This enables follow-up studies

Querying large treebanks : benchmarking GrETEL indexing

The amount of data that is available for research grows rapidly, yet technology to efficiently interpret and excavate these data lags behind. For instance, when using large treebanks for linguistic research, the speed of a query leaves much to be desired. GrETEL Indexing, or GrInding, tackles this issue. The idea behind GrInding is to make the search space as small as possible before actually starting the treebank search, by pre-processing the treebank at hand. We recursively divide the treebank into smaller parts, called subtree-banks, which are then converted into database files. All subtree-banks are organized according to their linguistic dependency pattern, and labeled as such. Additionally, general patterns are linked to more specific ones. By doing so, we create millions of databases, and given a linguistic structure we know in which databases that structure can occur, leading up to a significant efficiency boost. We present the results of a benchmark experiment, testing the effect of the GrInding procedure on the SoNaR-500 treebank