These are several macros I wrote to analyze single nanoparticle microscopy movies. These use Fiji/ImageJ and the MOSAIC 2D/3D particle tracker plugin. Ensure you have the MOSIAC suite installed into fiji before using. The file named ER track is optimized for tracking ER-GEMs in mammalian cells, please change the tracking parameters and file types to suit your needs.
These scripts can be run on a HPC cluster and submitted as a job for batch tracking files using a virtual frame buffer (XVFB, see the .sh file as an example SLURM submission).
Ref:
I. F. Sbalzarini and P. Koumoutsakos. Feature point tracking and trajectory analysis for video imaging in cell biology, J. Struct. Biol., 151(2):182-195, 2005
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., … Cardona, A. (2012). Fiji: an open-source platform for biological-image analysis. Nature Methods, 9(7), 676–682