Install EM Hole Finder » History » Revision 3
Revision 2 (Amber Herold, 08/26/2013 09:33 AM) → Revision 3/11 (Amber Herold, 08/26/2013 11:24 AM)
h1. Install EM Hole Finder The "EM Hole Finder" package is used for the Auto-masking feature of Appion. It automatically detects carbon edges in micrographs and creates masks for the images to hide the carbon portions. These masks can then be used to exclude particles in those regions from particle stacks. h2. Download em_hole_finder package The package is available at https://github.com/hbradlow/em_hole_finder h2. Set up a separate environment to run em_hole_finder em_hole_finder uses a version of numextension which is not compatible To use it with the rest of Appion. When the em_hole_finder program is called from Appion, it must first run an activation script to set up an appropriate environment for running em_hole_finder. h2. Set environment variables To call em_hole_finder from Appion, the installed package directory (em_hole_finder) needs to be in the user's PATH variable. Also, you need to set an environment variable "HOLE_FIND_ACTIVATE" to the path to the activate script. An example of the path is "/opt/em_hole_finder/env/bin" where a script called activate is located in the bin directory. path. ______ [[Install Protomo|< Install Protomo]] | [[Test Appion|Test Appion >]] ______