Ab initio nonrigid X-ray nanotomography

Michal Odstrcil,Silvia Vignolini,Alessandro Sepe,Mirko Holler,Christian G Schroer,Xiaoyuan Sheng,Manuel Guizar-Sicairos,Jörg Raabe

doi:10.1038/s41467-019-10670-7

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.

Highlights

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
Tomographic reconstruction of time-evolving samples is a challenging but important task that can help to understand dynamic processes inside a sample in a non-destructive way. 4D computed tomography (4D-CT) reconstruction methods[1] provide a significant gain in quality for time-evolving samples compared with simple sequential 3D reconstructions, these methods are often based on restrictive prior assumptions, such as periodicity of movement[1,2,3,4] or sparsity of the sample and its evolution[4,5,6,7]
Since the dynamic process is generally not known a priori, the evolution needs to be recovered from the measurements

Summary

Introduction

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. 4D computed tomography (4D-CT) reconstruction methods[1] provide a significant gain in quality for time-evolving samples compared with simple sequential 3D reconstructions, these methods are often based on restrictive prior assumptions, such as periodicity of movement[1,2,3,4] or sparsity of the sample and its evolution[4,5,6,7]. The generality of the 4D-CT methods, comes for the price of increased amount of reconstructed information and needs additional data, such as more tomographic projections or reconstruction constraints This is a severe limitation in many cases, when the dynamic processes in the sample are not of experimental interest and only lead to deteriorated reconstruction quality without providing any additional information. Instead of imposing additional constraints on the sample reconstruction, NCT is based on the assumption that the dynamic process acting upon the sample can be well described as an arbitrary deformation function that is smooth both temporally and spatially

Methods

Results

Conclusion