Challenges in imaging and predictive modeling of rhizosphere processes

Background Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes

A Spectral CT Method to Directly Estimate Basis Material Maps From Experimental Photon-Counting Data

The proposed spectral CT method solves the constrained one-step spectral CT reconstruction (cOSSCIR) optimization problem to estimate basis material maps while modeling the nonlinear X-ray detection process and enforcing convex constraints on the basis map images. In order to apply the optimization-based reconstruction approach to experimental data, the presented method empirically estimates the effective energy-window spectra using a calibration procedure. The amplitudes of the estimated spectra were further optimized as part of the reconstruction process to reduce ring artifacts. A validation approach was developed to select constraint parameters. The proposed spectral CT method was evaluated through simulations and experiments with a photon-counting detector. Basis material map images were successfully reconstructed using the presented empirical spectral modeling and cOSSCIR optimization approach. In simulations, the cOSSCIR approach accurately reconstructed the basis map images

A virtual world of paleontology

Computer-aided visualization and analysis of fossils has revolutionized the study of extinct organisms. Novel techniques allow fossils to be characterized in three dimensions and in unprecedented detail. This has enabled paleontologists to gain important insights into their anatomy, development, and preservation. New protocols allow more objective reconstructions of fossil organisms, including soft tissues, from incomplete remains. The resulting digital reconstructions can be used in functional analyses, rigorously testing long-standing hypotheses regarding the paleobiology of extinct organisms. These approaches are transforming our understanding of long-studied fossil groups, and of the narratives of organismal and ecological evolution that have been built upon them

Lose The Views: Limited Angle CT Reconstruction via Implicit Sinogram Completion

Computed Tomography (CT) reconstruction is a fundamental component to a wide variety of applications ranging from security, to healthcare. The classical techniques require measuring projections, called sinograms, from a full 180$^\circ$ view of the object. This is impractical in a limited angle scenario, when the viewing angle is less than 180$^\circ$, which can occur due to different factors including restrictions on scanning time, limited flexibility of scanner rotation, etc. The sinograms obtained as a result, cause existing techniques to produce highly artifact-laden reconstructions. In this paper, we propose to address this problem through implicit sinogram completion, on a challenging real world dataset containing scans of common checked-in luggage. We propose a system, consisting of 1D and 2D convolutional neural networks, that operates on a limited angle sinogram to directly produce the best estimate of a reconstruction. Next, we use the x-ray transform on this reconstruction to obtain a "completed" sinogram, as if it came from a full 180$^\circ$ measurement. We feed this to standard analytical and iterative reconstruction techniques to obtain the final reconstruction. We show with extensive experimentation that this combined strategy outperforms many competitive baselines. We also propose a measure of confidence for the reconstruction that enables a practitioner to gauge the reliability of a prediction made by our network. We show that this measure is a strong indicator of quality as measured by the PSNR, while not requiring ground truth at test time. Finally, using a segmentation experiment, we show that our reconstruction preserves the 3D structure of objects effectively.Comment: Spotlight presentation at CVPR 201