A set of BASH scripts and C++ programs representing a complete workflow for processing macro focus stacking photographs. Utilizes other open source packages (dcraw, Hugin, ImageMagick) internally. The Deadpixels script (automatic detection of dead and hot pixels in raw photographs) can be of use for general purpose photography, not just for macro photography.
The package should work under any Linux distro and under Cygwin (Windows). It will likely work under MacOS (not tested).
Consult the included README.txt file for installation instructions.
Detailed user guide can be found here:
http://pulsar124.wikia.com/wiki/Open_Source_workflow_for_macro_focus_stacking
boredmanicrobot: I have edited/will edit the shell scripts to be suitable for deployment on a FreeBSD system.