Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells

Version 1

nuc_ctDNA_process ImageJ 1.x macros and Matlab code for processing 3D nuclear classification and quantification. This repo is designed to help you recreate the methods use in the associated publication. Please don't hesitate to contact if you have questions. Happy to debug, update, etc if there's need.

Lif files: Use ImageJ 1.x macro in fiji folder to process lif files for subsequent ilastik and Matlab processing. Works with 3 channel data (DAPI, DIC, Rh-Red-X) and 4 channel data (DAPI, Cy5, Rh-Red-X, DIC). Generates .h5 or .tif files for ilastik raining, .jpgs for visualization and ROI overlays, and raw tif files for Matlab analysis.

Macro Usage Drag and drop; click Run and select .lif of interest. Only 3D data will be included, single layer images will be noted in output. A table of dimensions and max intensities is also created. Save .csv image info, and .txt output log for reference.