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

Image series analysis code used in "Tracking single adatoms in liquid in a Transmission Electron Microscope" <br> 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. <br> 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 <br> Script 8 was applied to all outputs from scripts 4-7. Generated various plots for each video, and initial processing of trajectory data. <br> 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.

《液体中单原子吸附剂在透射电子显微镜中的追踪》中使用的图像序列分析代码<br>脚本1-3适用于所有视频，采用通用设置。1_initial_processing——提取并制表元数据（Metadata），识别视频中放大倍数（magnification）不合适的帧并进行裁剪。2_PCA_denoise——基于补丁的主成分分析（PCA）降维以突出钼（Mo）晶格，详见SI（Supplementary Information）。3_filter_latticevid——对PCA去噪后的视频进行快速傅里叶变换（FFT）滤波和阈值处理。<br>脚本4-7适用于单个视频，采用个性化设置。需要大量参数调优才能获得合理的原子轨迹。本示例中，参数针对视频15.26.Scanning Preview.emi进行设置。4_filter_atomvid——手动裁剪（例如帧偏移显著或失焦时），随后对原始视频进行快速傅里叶变换（FFT）滤波和阈值处理以突出铂（Pt）吸附原子；5_driftcorrect——利用主成分分析（PCA）滤波输出中的已识别峰（钼位点）对所有视频进行漂移校正；6_lattice_points——使用PCA滤波视频识别并链接钼位点轨迹；7_adatom_points——使用FFT滤波视频识别并链接铂（Pt）吸附原子轨迹。<br>脚本8适用于脚本4-7的所有输出，为每个视频生成多种图表，并对轨迹数据进行初始处理。<br>最终脚本"compare"（含"compfunctions"中的函数）适用于脚本8的输出，包含高级处理及各视频轨迹间的比较。