M-TRACK is a live cell imaging analysis tool.
The package is written in Python 3.7. Parts of the source code are adapted from Celltool https://github.com/zpincus/celltool and https://github.com/Yurui-Li/Stay-Point-Identification.
requirement: wx numpy matplotlib sqlite3 argparse pandas sklearn Pillow mahotas scikit-image
The input file include: fluorescence images corresponding segmented cell mask images selected segmented cell mask image for calculation of mean cell contour database file (sqlite file) of cell tracking results (cellprofiler)
we share some data for test in the following link: https://drive.google.com/drive/folders/1KwVwR9moblQlA0U2aDPWHNeKDNONrk9J
Run MTRACK_GUI to start processing, select input folder and output folder
1 in morphology analysis, ptsnum is the number of points of cell outputline. This value depends on the resolution of images and requirements for analysis. Default is 150.
2 in Haralick analysis, fluor interval is the time step of fluorescence images depends on the experiment setting. Default is 1.
3 in trajectory analysis, minmum traj length is the lower threshold of trajectory length you want to analyze. Default is 12. After extraction of single cell trajectory and scaling analysis, choose an trajectory to plot from the folder.