In TrackMate after completing tracking, is there any way to export/save a movie with all tracks and moving spots (exactly as it appears after using the TrackMate)?
If you keep clicking on the Next button on the GUI, you will reach the last panel of the GUI, which collects miscellaneous actions.
One of them is called Capture TrackMate overlay and does what you need. It generates a RGB stack with the tracks burned-in. After that you have to export the stack to AVI and you are done.
Thanks a lot!