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

<p>Image series analysis code used in "Tracking single adatoms in liquid in a Transmission Electron Microscope"</p> <p><br></p> <p>Scripts 1-3 were applied to all videos with common settings.</p> <p>1_initial_processing - Extracting and tabulating Metadata, identifying frames from the videos where the megnification is not appropriate and cropping.</p> <p>2_PCA_denoise - Patch based PCA reduction to highlight Mo Lattice - see SI for details.</p> <p>3_filter_latticevid - FFT filtering and thresholding PCA denoised video.</p> <p><br></p> <p>Scripts 4-7 were applied to individual videos with individual settings. Significant parameter tuning was required to get reasonable atomic trajectories.</p> <p>In this example, parameters are set for the video 15.26.Scanning Preview.emi.</p> <p>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</p> <p>5_driftcorrect - Drift correction of all videos using identified peaks in the PCA filtered output (Mo Sites)</p> <p>6_lattice_points - Identification and linking of Mo Site trajectories, using PCA filtered video</p> <p>7_adatom_points - Identification and linking of Pt adatom trajectories, using FFT filtered video</p> <p><br></p> <p>Script 8 was applied to all outputs from scripts 4-7. Generated various plots for each video, and initial processing of trajectory data.</p> <p><br></p> <p>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.</p>