Image Stack Merger Plus is a plugin for ImageJ. As ImageJ, Image Stack Merger Plus is FREE and Open Source.
This ImageJ plugin permits from a video converted to image sequence to delete the moving subjects and create a clean background reference image. Then you will be able to sustract this reference image to all your sequence.
Download the archive file and extract it in your ImageJ plugin folder (usually C:\Program Files\ImageJ\plugins\ for Windows). Then restart ImageJ or use Help > Refresh Menus.