Appion

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.

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[[Install Protomo|< Install Protomo]] | [[Install SIMPLE|Install SIMPLE >]]

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