Install EM Hole Finder » History » Revision 10
Revision 9 (Amber Herold, 12/02/2013 02:39 PM) → Revision 10/11 (Sargis Dallakyan, 03/03/2014 01:15 PM)
h1. Install EM Hole Finder The "EM Hole Finder" package is used for the Auto-masking feature of Appion, available with version 3.0. 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. Installation Instructions for CentOS 6 em_hole_finder uses a version of numpy which is not compatible 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. The instructions below include installing a virtual environment package. Packages installed after sourcing the activate script will be used only for em_hole_finder while running within Appion. <pre> yum install git python-virtualenv libjpeg-devel -y easy_install pip cd /opt git clone https://github.com/hbradlow/em_hole_finder cd em_hole_finder virtualenv env source env/bin/activate pip install numpy pip install Cython pip install PIL pip install scipy pip install scikit-image pip install ipython pip install wsgiref </pre> h4. Make find_mask.py executable <pre> chmod +x find_mask.py </pre> 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. ______ [[Install Protomo|< Install Protomo]] | [[Install SIMPLE|Install SIMPLE >]] ______