Project

General

Profile

Install EM Hole Finder » History » Version 7

Amber Herold, 08/28/2013 02:26 PM

1 1 Amber Herold
h1. Install EM Hole Finder
2
3 6 Amber Herold
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.   
4 1 Amber Herold
5 3 Amber Herold
h2. Download em_hole_finder package
6 1 Amber Herold
7
The package is available at
8
9
https://github.com/hbradlow/em_hole_finder
10
11 4 Sargis Dallakyan
h2. Installation Instructions for CentOS 6
12
13 7 Amber Herold
em_hole_finder uses a version of numpy which is not compatible with the rest of Appion. 
14
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.
15
16 4 Sargis Dallakyan
<pre>
17 5 Sargis Dallakyan
yum install git python-virtualenv libjpeg-devel -y
18 4 Sargis Dallakyan
easy_install pip
19
cd /opt
20
git clone https://github.com/hbradlow/em_hole_finder
21
cd em_hole_finder
22
virtualenv env
23
source env/bin/activate
24
pip install numpy
25
pip install Cython
26
pip install PIL
27
pip install scipy
28
pip install scikit-image
29
pip install ipython
30 1 Amber Herold
pip install wsgiref
31 4 Sargis Dallakyan
</pre>
32
33
34 3 Amber Herold
35
h2. Set environment variables
36
37
To call em_hole_finder from Appion, the installed package directory (em_hole_finder) needs to be in the user's PATH variable.
38
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.
39 1 Amber Herold
40
______
41
42 2 Amber Herold
[[Install Protomo|< Install Protomo]] | [[Test Appion|Test Appion >]]
43 1 Amber Herold
44
______