Algorithm for the reconstruction of dynamic objects in CT-scanning using optical flow

Computed Tomography is a powerful imaging technique that allows non-destructive visualization of the interior of physical objects in different scientific areas. In traditional reconstruction techniques the object of interest is mostly considered to be static, which gives artefacts if the object is moving during the data acquisition. In this paper we present a method that, given only scan results of multiple successive scans, can estimate the motion and correct the CT-images for this motion assuming that the motion field is smooth over the complete domain using optical flow. The proposed method is validated on simulated scan data. The main contribution is that we show we can use the optical flow technique from imaging to correct CT-scan images for motion

Improving the reconstruction of dynamic processes by including prior knowledge

Visualizing and analyzing dynamic processes in 3 dimensions is an increasingly important topic. High-resolution CT-scanning is a suitable technique for this, as it is non-destructive and therefore does not hinder the dynamic process while it is advancing. However, CT reconstruction algorithms, which reconstruct a 3D volume from a series of projection images, assume a static sample. Motion artefacts are introduced when this assumption is invalid. This is usually solved by dividing the set of projection images in smaller subsets, each representing a time frame in which the change to the sample is assumed to be sufficiently small. Each subset can be reconstructed separately. However, due to the small size of the subsets and/or the high speed (and therefore lower statistics and higher noise) at which is scanned, the reconstruction quality is reduced. One method to improve reconstruction quality is using a priori knowledge. Of the two most used reconstruction algorithms, the iterative reconstruction scheme is best suited for this. The simultaneous algebraic reconstruction technique or SART starts from a (typically empty) volume and improves this gradually by back projecting the difference between a simulated projection from this volume and the measured projection. The resulting volume is used for the next iteration step. After a number of iterations, the solution converges to the final volume which represents the sample. In this research, this algorithm is used and adapted to take prior knowledge into account. Prior knowledge can take various forms. Using an initial volume (to start the reconstruction algorithm with) that resembles the sample is the most well-known and already presents a great improvement. This can be a volume that is reconstructed from a previous scan of the same sample, before the dynamic process is initiated, or one from after the process has finished. It is also possible to incorporate information in the algorithm about the regions in the volume where the changes are most likely to occur. The voxels in these regions are assigned a higher contribution from the back projection in comparison with their 'static' neighboring voxels which are assumed to be valid in the initial volume. This reduces the number of projections needed significantly. These forms of prior knowledge already pose a great improvement to the reconstruction quality, as is shown by the preliminary results. There are however numerous other possibilities to improve the reconstruction of dynamic processes. Other forms of prior knowledge, e.g. the continuity of changes or external measurements, can be included. Spatio-temporal correlations present another way to improve 4D-reconstruction. The projections will no longer be divided into completely separate subsets. Instead, the correlations between different projections will be used. This means that projections 'far' away from the time point that is being reconstructed will also (partially) be included. In this way the limitation of a small subset is (partially) removed, since much larger sets of projections are considered. The reconstructions that lie some time away from the reconstruction point cannot be straightforwardly included, since this would include exactly the artefacts that made the scanning of dynamic processes hard in the first place. This is a subject of further and current research. REFERENCES [1] M. Beister, D. Kolditz, W. A. Kalender, “Iterative reconstruction methods in X-ray CT,” Physica Medica, vol. 28, no. 2, pp. 94-108, Apr. 2012. [2] S. Berg, H. Ott, S. A. Klapp, A. Schwing, R. Neiteler, N. Brussee, A. Makurat, L. Leu, F. Enzmann, J.-O. Schwarz, “Real-time 3D imaging of Haines jumps in porous media flow,” Proc Natl Acad Sci U S A, vol. 110(10), pp. 3755–3759, Mar. 2013. [3] T. Bultreys, M. A. Boone, M. N. Boone, T. De Schryver, B. Masschaele, L. Van Hoorebeke, V. Cnudde, “Fast laboratory-based micro-computed tomography for pore-scale research: illustrative experiments and perspectives on the future,” Adv. Wat. Res., In Press. Available online May 2015. [4] V. Cnudde, M. N. Boone, “High-resolution X-ray computed tomography in geosciences: A review of the current technology and applications,” Earth-Science Reviews, vol. 123, pp. 1-17, Aug. 2013. [5] G. Van Eyndhoven, K. J. Batenburg, J. Sijbers, “Region-based iterative reconstruction of structurally changing objects in CT”, IEEE Trans. Image Processing, vol. 23, no. 2, pp. 909-919, Feb. 2014. [6] L. Brabant, “Latest developments in the improvement and quantification of high resolution X-ray tomography data,” Ph.D. dissertation, Dep. Phys. and Astr., Fac. Sciences, Ghent Univ., Ghent, Belgium, 2013

Region-based motion-compensated iterative reconstruction technique for dynamic computed tomography

Current state-of-the-art motion-based dynamic computed tomography reconstruction techniques estimate the deformation by considering motion models in the entire object volume although occasionally the proper change is local. In this article, we address this issue by introducing the region-based Motion-compensated Iterative Reconstruction Technique (rMIRT). It aims to accurately reconstruct the object being locally deformed during the scan, while identifying the deformed regions consistently with the motion models. Moreover, the motion parameters that correspond to the deformation in those areas are also estimated. In order to achieve these goals, we consider a mathematical optimization problem whose objective function depends on the reconstruction, the deformed regions and the motion parameters. The derivatives towards all of them are formulated analytically, which allows for efficient reconstruction using gradient-based optimizers. To the best of our knowledge, this is the first iterative reconstruction method in dynamic CT that exploits the analytical derivative towards the deformed regions.Comment: Accepted at ISBI 202

Knowledge Rich Natural Language Queries over Structured Biological Databases

Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity are undeniable for obvious reasons, their engineering is far from simple. In most part, semantics and intent preserving mapping of a well understood natural language query expressed over a structured database schema to a structured query language is still a difficult task, and research to tame the complexity is intense. In this paper, we propose a multi-level knowledge-based middleware to facilitate such mappings that separate the conceptual level from the physical level. We augment these multi-level abstractions with a concept reasoner and a query strategy engine to dynamically link arbitrary natural language querying to well defined structured queries. We demonstrate the feasibility of our approach by presenting a Datalog based prototype system, called BioSmart, that can compute responses to arbitrary natural language queries over arbitrary databases once a syntactic classification of the natural language query is made

An Iterative CT Reconstruction Algorithm for Fast Fluid Flow Imaging

The study of fluid flow through solid matter by computed tomography (CT) imaging has many applications, ranging from petroleum and aquifer engineering to biomedical, manufacturing, and environmental research. To avoid motion artifacts, current experiments are often limited to slow fluid flow dynamics. This severely limits the applicability of the technique. In this paper, a new iterative CT reconstruction algorithm for improved a temporal/spatial resolution in the imaging of fluid flow through solid matter is introduced. The proposed algorithm exploits prior knowledge in two ways. First, the time-varying object is assumed to consist of stationary (the solid matter) and dynamic regions (the fluid flow). Second, the attenuation curve of a particular voxel in the dynamic region is modeled by a piecewise constant function over time, which is in accordance with the actual advancing fluid/air boundary. Quantitative and qualitative results on different simulation experiments and a real neutron tomography data set show that, in comparison with the state-of-the-art algorithms, the proposed algorithm allows reconstruction from substantially fewer projections per rotation without image quality loss. Therefore, the temporal resolution can be substantially increased, and thus fluid flow experiments with faster dynamics can be performed

Ab initio nonrigid X-ray nanotomography

Abstract: Reaching the full potential of X-ray nanotomography, in particular for biological samples, is limited by many factors, of which one of the most serious is radiation damage. Although sample deformation caused by radiation damage can be partly mitigated by cryogenic protection, it is still present in these conditions and, as we exemplify here using a specimen extracted from scales of the Cyphochilus beetle, it will pose a limit to the achievable imaging resolution. We demonstrate a generalized tomographic model, which optimally follows the sample morphological changes and attempts to recover the original sample structure close to the ideal, damage-free reconstruction. Whereas our demonstration was performed using ptychographic X-ray tomography, the method can be adopted for any tomographic imaging modality. Our application demonstrates improved reconstruction quality of radiation-sensitive samples, which will be of increasing relevance with the higher brightness of 4th generation synchrotron sources