Volume imaging by tracking sparse topological features in electron micrograph tilt series

TY - JOUR

T1 - Volume imaging by tracking sparse topological features in electron micrograph tilt series

AU - Petersen, T. C.

AU - Zhao, C.

AU - Bøjesen, E. D.

AU - Broge, N. L.N.

AU - Hata, S.

AU - Liu, Y.

AU - Etheridge, J.

N1 - Publisher Copyright: © 2022 Elsevier B.V.

PY - 2022/6

Y1 - 2022/6

N2 - The sensitive coherent interference of electron waves arising from a specimen is useful for revealing subtle structural information in electron micrographs, which can be important for minimising dose and for rapid imaging. In general, dynamical diffraction is expected due to the useful strong interactions of electrons with matter, which can create phase contrast that violates the requisite Radon projection assumption for tomography. It is for these reasons that incoherent imaging modalities such as high angle annular dark field have been favoured to date in electron tomography of crystalline specimens, to access a monotonic relationship between specimen thickness and micrograph intensity. Here we use a geometric approach to track topological features that are robust to perturbation of the imaging conditions, to enable 3D reconstructions from electron microscope tilt series under imaging conditions that violate the Radon projection assumption, with an emphasis on phase contrast. Invoking a sparsity assumption, we demonstrate that topological features can be reliably tracked in 3D using a differential geometric form of stereoscopy, to circumvent departures from the projection approximation and reduce noise by effecting segmentation of interest points from the outset. We demonstrate this approach on a variety of different specimen and data types, from polyhedral nanoparticles, to steel dislocation networks, cryo-EM cellular structures and 3D diffuse diffraction of a relaxor ferroelectric.

AB - The sensitive coherent interference of electron waves arising from a specimen is useful for revealing subtle structural information in electron micrographs, which can be important for minimising dose and for rapid imaging. In general, dynamical diffraction is expected due to the useful strong interactions of electrons with matter, which can create phase contrast that violates the requisite Radon projection assumption for tomography. It is for these reasons that incoherent imaging modalities such as high angle annular dark field have been favoured to date in electron tomography of crystalline specimens, to access a monotonic relationship between specimen thickness and micrograph intensity. Here we use a geometric approach to track topological features that are robust to perturbation of the imaging conditions, to enable 3D reconstructions from electron microscope tilt series under imaging conditions that violate the Radon projection assumption, with an emphasis on phase contrast. Invoking a sparsity assumption, we demonstrate that topological features can be reliably tracked in 3D using a differential geometric form of stereoscopy, to circumvent departures from the projection approximation and reduce noise by effecting segmentation of interest points from the outset. We demonstrate this approach on a variety of different specimen and data types, from polyhedral nanoparticles, to steel dislocation networks, cryo-EM cellular structures and 3D diffuse diffraction of a relaxor ferroelectric.

KW - Dynamical diffraction

KW - Phase contrast

KW - Tomography

KW - Topology

KW - Transmission electron microscopy

U2 - 10.1016/j.ultramic.2022.113475

DO - 10.1016/j.ultramic.2022.113475

M3 - Journal article

C2 - 35255271

AN - SCOPUS:85125619432

SN - 0304-3991

VL - 236

JO - Ultramicroscopy

JF - Ultramicroscopy

M1 - 113475

ER -