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" 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.

发表于《透射电子显微镜中原位液体环境下单吸附原子的追踪》的图像序列分析代码说明如下：脚本1至3采用通用参数配置，应用于所有视频序列。
1_initial_processing：提取并制表元数据，识别视频中放大倍率不符合要求的帧并完成裁剪。
2_PCA_denoise：基于块的主成分分析（Principal Component Analysis, PCA）降维处理，以凸显钼（Mo）晶格细节，具体细节参见补充材料（SI）。
3_filter_latticevid：对经PCA降噪后的视频序列进行快速傅里叶变换（Fast Fourier Transform, FFT）滤波与阈值处理。
脚本4至7则针对单个视频序列采用专属参数配置，需经过大量参数调优方可获得合理的原子运动轨迹。本示例中，参数设置适配视频文件15.26.Scanning Preview.emi。
4_filter_atomvid：手动裁剪视频（如存在帧偏移显著或画面失焦的情况），随后对原始视频进行FFT滤波与阈值处理，以凸显铂（Pt）吸附原子。
5_driftcorrect：基于PCA降噪输出的钼位点峰值信息，对所有视频序列进行漂移校正。
6_lattice_points：利用PCA降噪后的视频序列，识别并关联钼位点的运动轨迹。
7_adatom_points：利用FFT滤波后的视频序列，识别并关联铂吸附原子的运动轨迹。
脚本8应用于脚本4至7生成的所有输出结果，为每个视频序列生成各类可视化图表，并完成轨迹数据的初步处理。
最终脚本`compare`（其功能函数封装于`compfunctions`中）应用于脚本8的输出结果，可实现进阶数据处理与各视频序列间的轨迹对比分析。