Install EM Hole Finder » History » Revision 5
Revision 4 (Sargis Dallakyan, 08/26/2013 12:38 PM) → Revision 5/11 (Sargis Dallakyan, 08/27/2013 01:54 PM)
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. Installation Instructions for CentOS 6
<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>
h2. Set up a separate environment to run em_hole_finder
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.
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.
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[[Install Protomo|< Install Protomo]] | [[Test Appion|Test Appion >]]
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