Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction
Abstract
Time-resolved imaging of molecules and materials made of light elements is an emerging field of transmission electron microscopy (TEM), and the recent development of direct electron detection cameras, capable of taking as many as 1,600 fps, has potentially broadened the scope of the time-resolved TEM imaging in chemistry and nanotechnology. However, such a high frame rate reduces electron dose per frame, lowers the signal-to-noise ratio (SNR), and renders the molecular images practically invisible. Here, we examined image noise reduction to take the best advantage of fast cameras and concluded that the Chambolle total variation denoising algorithm is the method of choice, as illustrated for imaging of a molecule in the 1D hollow space of a carbon nanotube with ~1 ms time resolution. Through the systematic comparison of the performance of multiple denoising algorithms, we found that the Chambolle algorithm improves the SNR by more than an order of magnitude when applied to TEM images taken at a low electron dose as required for imaging at around 1,000 fps. Open-source code and a standalone application to apply Chambolle denoising to TEM images and video frames are available for download.
- Authors:
-
[1];
- Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
- Univ. of Tokyo (Japan)
- Publication Date:
- Research Org.:
- Virginia Polytechnic Inst. and State University (Virginia Tech), Blacksburg, VA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1800341
- Grant/Contract Number:
- FG02-06ER15786
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Microscopy and Microanalysis
- Additional Journal Information:
- Journal Volume: 26; Journal Issue: 4; Journal ID: ISSN 1431-9276
- Publisher:
- Microscopy Society of America (MSA)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 47 OTHER INSTRUMENTATION; materials science; microscopy; denoising; image analysis; image processing; single-molecule imaging; transmission electron microscopy
Citation Formats
Stuckner, Joshua, Shimizu, Toshiki, Harano, Koji, Nakamura, Eiichi, and Murayama, Mitsuhiro. Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction. United States: N. p., 2020.
Web. doi:10.1017/s1431927620001750.
Stuckner, Joshua, Shimizu, Toshiki, Harano, Koji, Nakamura, Eiichi, & Murayama, Mitsuhiro. Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction. United States. https://doi.org/10.1017/s1431927620001750
Stuckner, Joshua, Shimizu, Toshiki, Harano, Koji, Nakamura, Eiichi, and Murayama, Mitsuhiro. Mon .
"Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction". United States. https://doi.org/10.1017/s1431927620001750. https://www.osti.gov/servlets/purl/1800341.
@article{osti_1800341,
title = {Ultra-Fast Electron Microscopic Imaging of Single Molecules With a Direct Electron Detection Camera and Noise Reduction},
author = {Stuckner, Joshua and Shimizu, Toshiki and Harano, Koji and Nakamura, Eiichi and Murayama, Mitsuhiro},
abstractNote = {Time-resolved imaging of molecules and materials made of light elements is an emerging field of transmission electron microscopy (TEM), and the recent development of direct electron detection cameras, capable of taking as many as 1,600 fps, has potentially broadened the scope of the time-resolved TEM imaging in chemistry and nanotechnology. However, such a high frame rate reduces electron dose per frame, lowers the signal-to-noise ratio (SNR), and renders the molecular images practically invisible. Here, we examined image noise reduction to take the best advantage of fast cameras and concluded that the Chambolle total variation denoising algorithm is the method of choice, as illustrated for imaging of a molecule in the 1D hollow space of a carbon nanotube with ~1 ms time resolution. Through the systematic comparison of the performance of multiple denoising algorithms, we found that the Chambolle algorithm improves the SNR by more than an order of magnitude when applied to TEM images taken at a low electron dose as required for imaging at around 1,000 fps. Open-source code and a standalone application to apply Chambolle denoising to TEM images and video frames are available for download.},
doi = {10.1017/s1431927620001750},
journal = {Microscopy and Microanalysis},
number = 4,
volume = 26,
place = {United States},
year = {Mon Jul 20 00:00:00 EDT 2020},
month = {Mon Jul 20 00:00:00 EDT 2020}
}
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