Automatic alignment for three-dimensional tomographic reconstruction

In tomographic reconstruction, the goal is to reconstruct an unknown object from a collection of line integrals. Given a complete sampling of such line integrals for various angles and directions, explicit inverse formulas exist to reconstruct the object. Given noisy and incomplete measurements, the inverse problem is typically solved through a regularized least-squares approach. A challenge for both approaches is that in practice the exact directions and offsets of the x-rays are only known approximately due to, e.g. calibration errors. Such errors lead to artifacts in the reconstructed image. In the case of sufficient sampling and geometrically simple misalignment, the measurements can be corrected by exploiting so-called consistency conditions. In other cases, such conditions may not apply and we have to solve an additional inverse problem to retrieve the angles and shifts. In this paper we propose a general algorithmic framework for retrieving these parameters in conjunction with an algebraic reconstruction technique. The proposed approach is illustrated by numerical examples for both simulated data and an electron tomography dataset

Regularized Newton Methods for X-ray Phase Contrast and General Imaging Problems

Like many other advanced imaging methods, x-ray phase contrast imaging and tomography require mathematical inversion of the observed data to obtain real-space information. While an accurate forward model describing the generally nonlinear image formation from a given object to the observations is often available, explicit inversion formulas are typically not known. Moreover, the measured data might be insufficient for stable image reconstruction, in which case it has to be complemented by suitable a priori information. In this work, regularized Newton methods are presented as a general framework for the solution of such ill-posed nonlinear imaging problems. For a proof of principle, the approach is applied to x-ray phase contrast imaging in the near-field propagation regime. Simultaneous recovery of the phase- and amplitude from a single near-field diffraction pattern without homogeneity constraints is demonstrated for the first time. The presented methods further permit all-at-once phase contrast tomography, i.e. simultaneous phase retrieval and tomographic inversion. We demonstrate the potential of this approach by three-dimensional imaging of a colloidal crystal at 95 nm isotropic resolution.Comment: (C)2016 Optical Society of America. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modifications of the content of this paper are prohibite

Transient growth in linearly stable Taylor-Couette flows

Non-normal transient growth of disturbances is considered as an essential prerequisite for subcritical transition in shear flows, i.e. transition to turbulence despite linear stability of the laminar flow. In this work we present numerical and analytical computations of linear transient growth covering all linearly stable regimes of Taylor--Couette flow. Our numerical experiments reveal comparable energy amplifications in the different regimes. For high shear Reynolds numbers Re the optimal transient energy growth always follows a 2/3-scaling with Re, which allows for large amplifications even in regimes where the presence of turbulence remains debated. In co-rotating Rayleigh-stable flows the optimal perturbations become increasingly columnar in their structure, as the optimal axial wavenumber goes to zero. In this limit of axially invariant perturbations we show that linear stability and transient growth are independent of the cylinders' rotation-ratio and we derive a universal 2/3-scaling of optimal energy growth with Re using WKB-theory. Based on this, a semi-empirical formula for the estimation of linear transient growth valid in all regimes is obtained.Comment: Published version: Revised according to JFM referee comments, incorporating various small corrections and clarifications compared to previous submission