Subsampling and inpainting approaches for electron tomography

Toby Sanders, Christian Dwyer

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

With the aim of addressing the issue of sample damage during electron tomography data acquisition, we propose a number of new reconstruction strategies based on subsampling (which uses only a subset of a full image) and inpainting (recovery of a full image from subsampled one). We point out that the total-variation (TV) inpainting model commonly used to inpaint subsampled images may be inappropriate for 2D projection images of typical TEM specimens. Thus, we propose higher-order TV (HOTV) inpainting, which accommodates the fact that projection images may be inherently smooth, as a more suitable image inpainting scheme. We also describe how the HOTV method can be extended to 3D, a scheme which makes use of both image data and sinogram data. Additionally, we propose gradient subsampling as a more efficient scheme than random subsampling. We make a rigorous comparison of our proposed new reconstruction schemes with existing ones. The new schemes are demonstrated to perform better than or as well as existing schemes, and we show that they outperform existing schemes at low subsampling rates.

Original languageEnglish (US)
Pages (from-to)292-302
Number of pages11
JournalUltramicroscopy
Volume182
DOIs
StatePublished - Nov 1 2017

Fingerprint

Tomography
Data acquisition
tomography
Transmission electron microscopy
Recovery
Electrons
electrons
projection
set theory
data acquisition
recovery
damage
gradients
transmission electron microscopy

Keywords

  • Electron tomography
  • Higher order methods
  • Inpainting
  • L1 regularization
  • Microscopy
  • Subsampling
  • Total variation

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Atomic and Molecular Physics, and Optics
  • Instrumentation

Cite this

Subsampling and inpainting approaches for electron tomography. / Sanders, Toby; Dwyer, Christian.

In: Ultramicroscopy, Vol. 182, 01.11.2017, p. 292-302.

Research output: Contribution to journalArticle

@article{b61e5cfb37634d0db779e7d4c6d7d7e9,
title = "Subsampling and inpainting approaches for electron tomography",
abstract = "With the aim of addressing the issue of sample damage during electron tomography data acquisition, we propose a number of new reconstruction strategies based on subsampling (which uses only a subset of a full image) and inpainting (recovery of a full image from subsampled one). We point out that the total-variation (TV) inpainting model commonly used to inpaint subsampled images may be inappropriate for 2D projection images of typical TEM specimens. Thus, we propose higher-order TV (HOTV) inpainting, which accommodates the fact that projection images may be inherently smooth, as a more suitable image inpainting scheme. We also describe how the HOTV method can be extended to 3D, a scheme which makes use of both image data and sinogram data. Additionally, we propose gradient subsampling as a more efficient scheme than random subsampling. We make a rigorous comparison of our proposed new reconstruction schemes with existing ones. The new schemes are demonstrated to perform better than or as well as existing schemes, and we show that they outperform existing schemes at low subsampling rates.",
keywords = "Electron tomography, Higher order methods, Inpainting, L1 regularization, Microscopy, Subsampling, Total variation",
author = "Toby Sanders and Christian Dwyer",
year = "2017",
month = "11",
day = "1",
doi = "10.1016/j.ultramic.2017.07.021",
language = "English (US)",
volume = "182",
pages = "292--302",
journal = "Ultramicroscopy",
issn = "0304-3991",
publisher = "Elsevier",

}

TY - JOUR

T1 - Subsampling and inpainting approaches for electron tomography

AU - Sanders, Toby

AU - Dwyer, Christian

PY - 2017/11/1

Y1 - 2017/11/1

N2 - With the aim of addressing the issue of sample damage during electron tomography data acquisition, we propose a number of new reconstruction strategies based on subsampling (which uses only a subset of a full image) and inpainting (recovery of a full image from subsampled one). We point out that the total-variation (TV) inpainting model commonly used to inpaint subsampled images may be inappropriate for 2D projection images of typical TEM specimens. Thus, we propose higher-order TV (HOTV) inpainting, which accommodates the fact that projection images may be inherently smooth, as a more suitable image inpainting scheme. We also describe how the HOTV method can be extended to 3D, a scheme which makes use of both image data and sinogram data. Additionally, we propose gradient subsampling as a more efficient scheme than random subsampling. We make a rigorous comparison of our proposed new reconstruction schemes with existing ones. The new schemes are demonstrated to perform better than or as well as existing schemes, and we show that they outperform existing schemes at low subsampling rates.

AB - With the aim of addressing the issue of sample damage during electron tomography data acquisition, we propose a number of new reconstruction strategies based on subsampling (which uses only a subset of a full image) and inpainting (recovery of a full image from subsampled one). We point out that the total-variation (TV) inpainting model commonly used to inpaint subsampled images may be inappropriate for 2D projection images of typical TEM specimens. Thus, we propose higher-order TV (HOTV) inpainting, which accommodates the fact that projection images may be inherently smooth, as a more suitable image inpainting scheme. We also describe how the HOTV method can be extended to 3D, a scheme which makes use of both image data and sinogram data. Additionally, we propose gradient subsampling as a more efficient scheme than random subsampling. We make a rigorous comparison of our proposed new reconstruction schemes with existing ones. The new schemes are demonstrated to perform better than or as well as existing schemes, and we show that they outperform existing schemes at low subsampling rates.

KW - Electron tomography

KW - Higher order methods

KW - Inpainting

KW - L1 regularization

KW - Microscopy

KW - Subsampling

KW - Total variation

UR - http://www.scopus.com/inward/record.url?scp=85026816340&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85026816340&partnerID=8YFLogxK

U2 - 10.1016/j.ultramic.2017.07.021

DO - 10.1016/j.ultramic.2017.07.021

M3 - Article

VL - 182

SP - 292

EP - 302

JO - Ultramicroscopy

JF - Ultramicroscopy

SN - 0304-3991

ER -