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Oblique reconstructions in tomosynthesis. I. Linear systems theory.

ABSTRACT: By convention, slices in a tomosynthesis reconstruction are created on planes parallel to the detector. It has not yet been demonstrated that slices can be generated along oblique directions through the same volume, analogous to multiplanar reconstructions in computed tomography (CT). The purpose of this work is to give a proof-of-principle justification for oblique reconstructions in tomosynthesis, which acquires projection images over a smaller angular range than CT.To investigate the visibility of individual frequencies in an oblique reconstruction, a theoretical framework is developed in which the reconstruction of a sinusoidal input is calculated. The test frequency is pitched at an angle in a 2D parallel-beam acquisition geometry. Reconstructions are evaluated along the pitch of the object. The modulation transfer function (MTF) is calculated from the relative signal at various test frequencies. The MTF determines whether modulation is within detectable limits in oblique reconstructions. In the previous linear systems (LS) model [B. Zhao and W. Zhao, "Three-dimensional linear system analysis for breast tomosynthesis," Med. Phys. 35(12), 5219-5232 (2008)], the MTF was calculated only in reconstructed slices parallel to the detector. This paper generalizes the MTF calculation to reconstructed slices at all possible pitches. Unlike the previous LS model, this paper also analyzes the effect of object thickness on the MTF. A second test object that is considered is a rod whose long axis is pitched similar to the sinusoidal input. The rod is used to assess whether the length of an object can be correctly estimated in oblique reconstructions.To simulate the conventional display of the reconstruction, slices are first created along a 0° pitch. This direction is perpendicular to the rays of the central projection. The authors show that the input frequency of a pitched sinusoidal object cannot be determined using these slices. By changing the pitch of the slice to match the object, it is shown that the input frequency is properly resolved. To prove that modulation is preserved in pitched slices, the MTF is also calculated. Modulation is within detectable limits over a broad range of pitches if the object is thin, but is detectable over a narrower range of pitches if the object is thick. Turning next to the second test object, it is shown that the length of a pitched rod can be correctly determined in oblique reconstructions. Concordant with the behavior of the MTF, the length estimate is accurate over a broad range of pitches if the object is thin, but is correct over a narrower range of pitches if the object is thick.This work justifies the feasibility of oblique reconstructions in tomosynthesis. It is demonstrated that pitched test objects are most easily visualized with oblique reconstructions instead of conventional reconstructions. In order to achieve high image quality over a broad range of pitches, the object must be thin. By analyzing the effect of reconstruction pitch and object thickness on image quality, this paper generalizes the previous LS model for tomosynthesis.

SUBMITTER: Acciavatti RJ

PROVIDER: S-EPMC3808438 | biostudies-other | 2013 Nov

REPOSITORIES: biostudies-other

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Project description:In tomosynthesis, super-resolution has been demonstrated using reconstruction planes parallel to the detector. Super-resolution allows for subpixel resolution relative to the detector. The purpose of this work is to develop an analytical model that generalizes super-resolution to oblique reconstruction planes.In a digital tomosynthesis system, a sinusoidal test object is modeled along oblique angles (i.e., "pitches") relative to the plane of the detector in a 3D divergent-beam acquisition geometry. To investigate the potential for super-resolution, the input frequency is specified to be greater than the alias frequency of the detector. Reconstructions are evaluated in an oblique plane along the extent of the object using simple backprojection (SBP) and filtered backprojection (FBP). By comparing the amplitude of the reconstruction against the attenuation coefficient of the object at various frequencies, the modulation transfer function (MTF) is calculated to determine whether modulation is within detectable limits for super-resolution. For experimental validation of super-resolution, a goniometry stand was used to orient a bar pattern phantom along various pitches relative to the breast support in a commercial digital breast tomosynthesis system.Using theoretical modeling, it is shown that a single projection image cannot resolve a sine input whose frequency exceeds the detector alias frequency. The high frequency input is correctly visualized in SBP or FBP reconstruction using a slice along the pitch of the object. The Fourier transform of this reconstructed slice is maximized at the input frequency as proof that the object is resolved. Consistent with the theoretical results, experimental images of a bar pattern phantom showed super-resolution in oblique reconstructions. At various pitches, the highest frequency with detectable modulation was determined by visual inspection of the bar patterns. The dependency of the highest detectable frequency on pitch followed the same trend as the analytical model. It was demonstrated that super-resolution is not achievable if the pitch of the object approaches 90°, corresponding to the case in which the test frequency is perpendicular to the breast support. Only low frequency objects are detectable at pitches close to 90°.This work provides a platform for investigating super-resolution in oblique reconstructions for tomosynthesis. In breast imaging, this study should have applications in visualizing microcalcifications and other subtle signs of cancer.

Project description:In the past decade, over 50 genome-scale metabolic reconstructions have been built for a variety of single- and multi- cellular organisms. These reconstructions have enabled a host of computational methods to be leveraged for systems-analysis of metabolism, leading to greater understanding of observed phenotypes. These methods have been sparsely applied to comparisons between multiple organisms, however, due mainly to the existence of differences between reconstructions that are inherited from the respective reconstruction processes of the organisms to be compared. To circumvent this obstacle, we developed a novel process, termed metabolic network reconciliation, whereby non-biological differences are removed from genome-scale reconstructions while keeping the reconstructions as true as possible to the underlying biological data on which they are based. This process was applied to two organisms of great importance to disease and biotechnological applications, Pseudomonas aeruginosa and Pseudomonas putida, respectively. The result is a pair of revised genome-scale reconstructions for these organisms that can be analyzed at a systems level with confidence that differences are indicative of true biological differences (to the degree that is currently known), rather than artifacts of the reconstruction process. The reconstructions were re-validated with various experimental data after reconciliation. With the reconciled and validated reconstructions, we performed a genome-wide comparison of metabolic flexibility between P. aeruginosa and P. putida that generated significant new insight into the underlying biology of these important organisms. Through this work, we provide a novel methodology for reconciling models, present new genome-scale reconstructions of P. aeruginosa and P. putida that can be directly compared at a network level, and perform a network-wide comparison of the two species. These reconstructions provide fresh insights into the metabolic similarities and differences between these important Pseudomonads, and pave the way towards full comparative analysis of genome-scale metabolic reconstructions of multiple species.

Project description:In digital breast tomosynthesis (DBT), a volumetric reconstruction of the breast is generated from a limited range of x-ray projections. One trade-off of DBT is resolution loss in the projections due to non-normal (i.e., oblique) x-ray incidence. Although degradation in image quality due to oblique incidence has been studied using empirical data and Monte Carlo simulations, a theoretical treatment has been lacking. The purpose of this work is to extend Swank's calculations of the transfer functions of turbid granular phosphors to oblique incidence. The model is ultimately used as a tool for optimizing the design of DBT detectors.A quantum-limited system and 20 keV x-rays are considered. Under these assumptions, the modulation transfer function (MTF) and noise power spectra (NPS) are derived using the diffusion approximation to the Boltzmann equation to model optical scatter within the phosphor. This approach is applicable to a nonstructured scintillator such as gadolinium oxysulfide doped with terbium (Gd(2)O(2)S:Tb), which is commonly used in breast imaging and which can reasonably approximate other detector materials. The detective quantum efficiency (DQE) is then determined from the Nishikawa formulation, where it is written as the product of the x-ray quantum detection efficiency, the Swank factor, and the Lubberts fraction. Transfer functions are calculated for both front- and back-screen configurations, which differ by positioning the photocathode at the exit or entrance point of the x-ray beam, respectively.In the front-screen configuration, MTF and DQE are found to have considerable angular dependence, while NPS is shown to vary minimally with projection angle. As expected, the high frequency MTF and DQE are degraded substantially at large angles. By contrast, all transfer functions for the back-screen configuration have the advantage of significantly less angular dependence. Using these models, we investigated the possibility for optimizing the design of DBT detectors. As an example optimization strategy, the phosphor thickness which maximizes the DQE at a fixed frequency is analyzed. This work demonstrates that the optimal phosphor thickness for the front-screen is angularly dependent, shifting to lower thickness at higher angles. Conversely, the back-screen is not optimized by a single thickness but instead attains reasonably high DQE values over a large range of thicknesses. Although the back-screen configuration is not suited for current detectors using a glass substrate, it may prove to be preferred in future detectors using newly proposed plastic thin-film transistor (TFT) substrates.Using the diffusion approximation to the Boltzmann equation to model the spread of light in a scintillator, this paper develops an analytical model of MTF, NPS, and DQE for a phosphor irradiated obliquely. The model is set apart from other studies on oblique incidence in being derived from first principles. This work has applications in the optimization of DBT detector design.

Project description:Almost every biomedical systems analysis requires early decisions regarding the choice of the most suitable representations to be used. De facto the most prevalent choice is a system of ordinary differential equations (ODEs). This framework is very popular because it is flexible and fairly easy to use. It is also supported by an enormous array of stand-alone programs for analysis, including many distinct numerical solvers that are implemented in the main programming languages. Having selected ODEs, the modeler must then choose a mathematical format for the equations. This selection is not trivial as nearly unlimited options exist and there is seldom objective guidance. The typical choices include ad hoc representations, default models like mass-action or Lotka-Volterra equations, and generic approximations. Within the realm of approximations, linear models are typically successful for analyses of engineered systems, but they are not as appropriate for biomedical phenomena, which often display nonlinear features such as saturation, threshold effects or limit cycle oscillations, and possibly even chaos. Power-law approximations are simple but overcome these limitations. They are the key ingredient of Biochemical Systems Theory (BST), which uses ODEs exclusively containing power-law representations for all processes within a model. BST models cover a vast repertoire of nonlinear responses and, at the same time, have structural properties that are advantageous for a wide range of analyses. Nonetheless, as all ODE models, the BST approach has limitations. In particular, it is not always straightforward to account for genuine discreteness, time delays, and stochastic processes. As a new option, we therefore propose here an alternative to BST in the form of discrete Biochemical Systems Theory (dBST). dBST models have the same generality and practicality as their BST-ODE counterparts, but they are readily implemented even in situations where ODEs struggle. As a case study, we illustrate dBST applied to the dynamics of the aryl hydrocarbon receptor (AhR), a signal transduction system that simultaneously involves time delays and stochasticity.

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Oblique reconstructions in tomosynthesis. I. Linear systems theory.

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