As X-ray imaging is pushed further into the nanoscale, the sample deformations due to the increased radiation levels or mechanical instabilities of the microscopes become more apparent, leading to challenges in realizing high-resolution microscopy under these conditions. Here we propose a distributed optimization solver for imaging of samples at the nanoscale. Our approach solves the tomography and ptychography problems jointly with projection data alignment, nonrigid sample deformation correction, and regularization. Applicability of the method is demonstrated on experimental data sets from the Transmission X-ray Microscope, and the hard X-ray nanoprobe.
KEYWORDS: X-rays, Microscopes, Materials science, Spatial resolution, Zone plates, Systems engineering, Software development, Reconstruction algorithms, Data acquisition, 3D acquisition
A new Transmission X-ray Microscope (TXM), optimized for in-situ nano-tomography experiments, has been designed and built at the Advanced Photon Source (APS). The instrument has been in operation for the last two years and is supporting users over large fields of Science, from energy storage and material science to natural sciences. The flexibility of our X-ray microscope design permits evolutionary geometries and can accommodate relatively heavy, up to 5 kg, and bulky in-situ cells while ensuring high spatial resolution, which is expected to improve steadily thanks to the support of the RD program led by the APS-Upgrade project on Fresnel zone plates (FZP). The robust sample stack, designed with minimum degrees of freedom shows a stability better than 4 nm rms at the sample location. The TXM operates with optics fabricated in-house. A spatial resolution of 30 nm per voxel has been demonstrated when the microscope operates with a 60 nm outermost zone width FZP with a measured efficiency of 18% at 8 keV. 20 nm FZP are also currently available and should be in routine use within the next few months once a new matching condenser is produced. In parallel, efficiency is being improved with opto-mechanical engineering (FZP stacking system) and software developments (more efficient reconstruction algorithms combined with different data acquisition schemes), enabling 3D dynamic studies when sample evolution occurs within a couple of tens of seconds.
Propagation-based X-ray phase-contrast tomography (XPCT) provides the opportunity to image weakly absorbing objects and is being explored actively for a variety of important pre-clinical applications. Quantitative XPCT image reconstruction methods typically involve a phase retrieval step followed by application of an image reconstruction algorithm. Most approaches to phase retrieval require either acquiring multiple images at different object-to-detector distances or introducing simplifying assumptions, such as a single-material assumption, to linearize the imaging model. In order to overcome these limitations, a non-linear image reconstruction method has been proposed previously that jointly estimates the absorption and refractive properties of an object from XPCT projection data acquired at a single propagation distance, without the need to linearize the imaging model. However, the numerical properties of the associated non-convex optimization problem remain largely unexplored. In this study, computer simulations are conducted to investigate the feasibility of the joint reconstruction problem in practice. We demonstrate that the joint reconstruction problem is ill-posed and sensitive to system inconsistencies. Particularly, the method can generate accurate refractive index images only if the object is thin and has no phase-wrapping in the data. However, we also observed that, for weakly absorbing objects, the refractive index images reconstructed by the joint reconstruction method are, in general, more accurate than those reconstructed using methods that simply ignore the object’s absorption.
Analysis of large tomographic datasets at synchrotron light sources is becoming progressively more challenging due to the increasing data acquisition rates that new technologies in X-ray sources and detectors enable. The next generation of synchrotron facilities that are currently under design or construction throughout the world will provide diffraction limited X-ray sources and is expected to boost the current data rates by several orders of magnitude and stressing the need for the development and integration of efficient analysis tools more than ever. Here we describe in detail an attempt to provide such a collaborative framework for the analysis of synchrotron tomographic data that has the potential to unify the effort of different facilities and beamlines performing similar tasks. The proposed Python/C++ based framework is open-source, OS and data format independent, parallelizable and supports functional programming that many researchers prefer. This collaborative platform will affect all major synchrotron facilities where new effort is now dedicated into developing new tools that can be deployed at the facility for real time processing as well as distributed to users for off site data processing.
Using solutions of spectral transport-of-intensity equations, we have demonstrated a single step method to
retrieve absorption and phase changes for a wide range of x-ray imaging energies and material composition. We
simulated a Cadmium-Zinc-Telluride based spectral detection system using a cascade model for investigations of
breast mass and microcalcification detectability when using both absorption and phase images simultaneously.
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