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.
Highlights
Video recording of molecular motions and chemical reactions with a single-molecule atomic-resolution real-time transmission electron microscopic (SMART-EM) technique has emerged as a new technology for the study of mobile molecules and nanoscale assemblies (Nakamura, 2017)
The C60@CNT1 and C60@CNT2 datasets, recorded at an electron dose per image ranging from 0.5 × 105 to 65 × 105 electrons/nm2, were used to evaluate the performance of the denoising algorithms in increasing the signal-to-noise ratio (SNR) while preserving the signal
Aberration-corrected transmission electron microscopy (TEM) have significantly increased the spatial resolution of SMART-EM imaging, while high frame rate complementary metal oxide semiconductor (CMOS) cameras have reduced the temporal resolution to the 1 ms range
Summary
Video recording of molecular motions and chemical reactions with a single-molecule atomic-resolution real-time transmission electron microscopic (SMART-EM) technique has emerged as a new technology for the study of mobile molecules and nanoscale assemblies (Nakamura, 2017). The in situ kinetic study of chemical reactions (Okada et al, 2017), mechanistic investigation of molecular crystal formation (Harano et al, 2012), and capturing and analyzing minute reaction intermediates (Xing et al, 2019) have illustrated the potential of the SMART-EM methodology in chemistry and nanoscience. This video technology has posed a new challenge of acquiring video images of fast moving or reacting molecules, so that we can visually and quantitatively study the dynamics of the observed chemical events. We need the highest possible frame rate with the highest possible image contrast
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