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Analysis Code from "Tracking single adatoms in liquid in a Transmission Electron Microscope"

Version 2 2022-07-27, 13:48
Version 1 2022-07-27, 13:48
posted on 2022-07-27, 13:48 authored by Nicholas ClarkNicholas Clark

Image series analysis code used in "Tracking single adatoms in liquid in a Transmission Electron Microscope"

Scripts 1-3 were applied to all videos with common settings.

1_initial_processing - Extracting and tabulating Metadata, identifying frames from the videos where the megnification is not appropriate and cropping.

2_PCA_denoise - Patch based PCA reduction to highlight Mo Lattice - see SI for details.

3_filter_latticevid - FFT filtering and thresholding PCA denoised video.

Scripts 4-7 were applied to individual videos with individual settings. Significant parameter tuning was required to get reasonable atomic trajectories.

In this example, parameters are set for the video 15.26.Scanning Preview.emi.

4_filter_atomvid - Manual cropping (eg if frame shifted significantly, or frames were out of focus), then FFT filtering and thresholding original video to highlight Pt adatoms

5_driftcorrect - Drift correction of all videos using identified peaks in the PCA filtered output (Mo Sites)

6_lattice_points - Identification and linking of Mo Site trajectories, using PCA filtered video

7_adatom_points - Identification and linking of Pt adatom trajectories, using FFT filtered video

Script 8 was applied to all outputs from scripts 4-7. Generated various plots for each video, and initial processing of trajectory data.

The final script "compare" with functions contained in "compfunctions" was applied to outputs from 8. Contained advanced processing, and comparisons between trajectories for each video.


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