Make sure that the movie you are working on is saved as an ImageJ tiff, and before resaving it, ensures that the calibration (pixel size and frame interval) is correct.
Then launch the
Manual tracking with Trackmate plugin on the opened image.
There is a save button at the bottom-left part of the GUI. It will generate a possibly large XML file. You will be able to reload it later using the
Load TtrackMate file plugin. It will reopen the image on the fly, if it was properly saved.