About the script

About The Script (tracking.py)

This script was initially written for Andreas Papadopulos of Fred Meunier's lab to automate analysis of particle tracking data exported from Metamorph. A GUI was developed to assist with managing the configuration and further functionality was added to assist with reviewing and filtering particle tracking data for further analysis.

INPUT:

The input is either a Metamorph (trc) or CSV file (comma delimited) with a full set of particle tracking data. (For format, see Instructions)

SCRIPT PROCESSING:

The x,y coordinates are rounded and the distance travelled by each particle at that coordinate pair is averaged to produce polar coordinates showing mean velocity. This data is presented as a quiver plot. The data may be filtered by only including tracks of a minimum number of points or minimum and maximum track length. Each track can be reviewed with its corresponding Cumulative square distance or Mean square distance (Diffusion coefficient) and selected for export for further analysis. A region of interest (ROI) can be selected from the total plot, and the particles whose track positions lie within these coordinates are presented as a heatmap of particle speed.

OUTPUT:

The total, ROI heatmap and individual quiver plots can be saved as png files. Data outputs for all, filtered, ROI and reviewed plots can be saved in CSV format.

Any issues or suggestions - please contact Liz Cooper-Williams, QBI (e.cooperwilliams@uq.edu.au)