examples/tomotrackbox.py
This program expects a tomographic tilt-series as input. Normally this would be the .ali file resulting from a tilt-series alignment in IMOD, but technically the program can do some of its own alignment, so if your raw tilt-series is not TOO far out of alignment, you can still use this program. It does not require fiducials as the reconstructed feature itself acts as a fiducial.
example usage: $EMAN2DIR/examples/tomotrackbox.py aligned_stack.ali --invert
(use --invert if the target of interest looks black on a lighter background when normally viewed. EMAN2 requires white on a dark background.)
Here is a short demo movie showing how to use some of its features: