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A lot of stereoscopic cameras use the .MPO format to store two JPEG images, including the Fuji W1, W3, and a few 3D camcorders that have a still mode. It can do two things for you: it can separate out the image files into a left and right pair, so you can process them or do whatever you want with them, or it can create an anaglyphic image (the ones you need coloured glasses to view). It is simple to use from the command line and takes wildcards, so you could process a whole batch of files with: mungempo *.MPO.