Improving magnetic STEM-differential phase contrast imaging using precession

<p>Scanning transmission electron microscopy datasets and processing files&nbsp;used in the journal publication &quot;<strong>Improving Magnetic STEM-Differential Phase Contrast Imaging using Precession</strong>&quot;.</p> <p>DOI link to publication:&nbsp;<a href="https://doi.org/10.1093/micmic/ozad001">https://doi.org/10.1093/micmic/ozad001</a></p> <p>&nbsp;</p> <p><strong>Prerequisites</strong></p> <p>To run the scripts necessary to process the files, the open source packages JupyterLab, HyperSpy, pyXem, and fpd need to be installed. These notebooks were created with these package versions:</p> <ul> <li>hyperspy 1.6.4</li> <li>pyxem 0.13.3</li> <li>fpd 0.2.0</li> <li>jupyterlab 3.2.0</li> </ul> <p>&nbsp;</p> <p><strong>Data files and processing scripts</strong></p> <p>Data files are collected in .zip folders and have names that start with &quot;d00..&quot;, while processing scripts are in the Jupyter Notebook .ipynb data format whose names start with &quot;p00..&quot;. These files are divided into three main processing steps, outlined as follows:</p> <ol> <li><strong>Processing of raw data</strong>: Raw data files can be found in the d001_scans.zip folder. These are processed with the p002_get_dpc_raw.ipynb script which uses either the center of mass or phase correlation methods.</li> <li><strong>D-scan correction</strong>: The processed files from the previous step are saved in the d002_dpc_raw.zip folder. The p003_get_dpc_cor.ipynb script performs a d-scan correction on these files and saves the output in the&nbsp;d003_dpc_cor.zip folder. <ul> <li><strong>Virtual segmented detector algorithm</strong>: For comparison purposes to the other processing algorithms, a virtual segmented detector algorithm was developed and can be found in the p004_segmented_detector.ipynb script. This algorithm extracts a linear d-scan plane from already processed phase correlation files found in d002_dpc_raw.zip, subtracts it from the raw data files found in d001_scans.zip, and finally performs the processing algorithm.</li> </ul> </li> <li><strong>Plotting files</strong>:<strong>&nbsp;</strong>The p005_plot_dpc_images.ipynb script creates the figures as seen in the journal publication. The input files are those found in d003_dpc_cor.zip from the previous processing step.</li> </ol>