Two-Stage Alignment of FIB-SEM Images of Rock Samples.

Iryna Reimers,Ilia Safonov,Ivan Yakimchuk,Anton Kornilov

doi:10.3390/jimaging6100107

Abstract

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) tomography provides a stack of images that represent serial slices of the sample. These images are displaced relatively to each other, and an alignment procedure is required. Traditional methods for alignment of a 3D image are based on a comparison of two adjacent slices. However, such algorithms are easily confused by anisotropy in the sample structure or even experiment geometry in the case of porous media. This may lead to significant distortions in the pore space geometry, if there are no stable fiducial marks in the frame. In this paper, we propose a new method, which meaningfully extends existing alignment procedures. Our technique allows the correction of random misalignments between slices and, at the same time, preserves the overall geometrical structure of the specimen. We consider displacements produced by existing alignment algorithms as a signal and decompose it into low and high-frequency components. Final transformations exclude slow variations and contain only high frequency variations that represent random shifts that need to be corrected. The proposed algorithm can operate with not only translations but also with arbitrary affine transformations. We demonstrate the performance of our approach on a synthetic dataset and two real FIB-SEM images of natural rock.

Highlights

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) is a powerful technique for 3D serial imaging at the nanoscale
In the case of available ground truth (GT), that is, when the correct displacements are known, the obvious way to evaluate the quality of alignment is to calculate the arithmetical mean of differences between them and those found by the algorithm (Normalized Absolute Differences): n
Conventional alignment algorithms introduce distortions in FIB-SEM images because they are confused by internal structures that are not oriented along the direction of the electron beam and pore-back effect in certain cases

Summary

Introduction

Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) is a powerful technique for 3D serial imaging at the nanoscale. In the FIB column, there is a source of ions, which are accelerated and focused into the beam Striking the sample, they sputter atoms from the surface and, in such a way, etch the specimen. After the ion beam removes a thin layer of substance from the sample, the electron microscope scans the surface at an angle that usually equals 52 degrees. Multiple repetitions of these two operations produce a stack of images that correspond to serial slices of a sample. The advanced Digital Rock methodology consists of simulation on various scales including the nanoscale [10,11]

Methods

Results

Conclusion