Tutorial for the xsPT particle tracker plug-in of ImageJ, part one

The instructor introduces the xsPT particle tracker plugin for ImageJ/Fiji and explains the initial requirements. A multichannel image with time dimension is opened and the appropriate channel is selected before launching the plugin from the Plugins > Tracking menu.

The instructor explains the background filter size parameter, which represents the average particle diameter radius in pixels, and the dynamics parameter that identifies particles based on local maxima intensity relative to overall pixel distribution. The dynamics value determines the percentile threshold for particle detection.

The sensitivity parameter is explained as controlling whether touching objects remain separated or merge, with values from 0.5 to 1. The instructor also describes available noise filter options and checks the background polarity setting for this particular image.

The instructor clicks preview to visualize particle detection, showing genuine particles in green and merged particles in yellow. Dynamic adjustments are made to the dynamics and signal-to-background values to optimize particle recognition.

The cutoff frequency parameter controls what fraction of the detected signal defines particle boundaries. Lower values produce larger particles while higher values create smaller particles, and the instructor demonstrates this parameter's effect on particle visualization.

The geometric center checkbox is explained as a faster but less accurate alternative to 2D Gaussian centroid fitting. The instructor then describes tracking parameters including maximum displacement, step penalty, and ghost particle inclusion options.

After confirming all parameter settings, the instructor clicks the go button to run the plugin and initiate the particle tracking process.