This repo stores some scripts used in the publication 'Single-molecule phenotyping and in-situ sequencing for mechanistic analysis of protein-DNA interactions and reactions'. The scripts used for base calling, localization counting, and the preprocessing including steps such as drift correction (AIM method), channel registration are in the correspondingly named .py files. We use picasso (https://github.com/jungmannlab/picasso) as backend for localization detection & fitting. The pystackreg(https://github.com/glichtner/pystackreg) for registeration.
Please notice that since these scripts are tailored to our experiment, parameters such as camera baseline, gain, ROI, penalty for PELT algorithm etc. need to be changed directly in the codes before they can be used in other experiments. After adjusting, they can be used just by providing the addresses of corresponding files such as movies in .tif format, localizations generated by Picasso in .hdf5 format, and .csv files. We may provide a standalone software or napari plugin if it's a popular demand.