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Scipion plugin to integrate Topaz particle picker
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README.rst

Topaz plugin

This plugin allows to use Topaz programs within the Scipion framework. It will allow to pre-process micrographs and pick particles within Scipion.

Topaz is a pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples.

Setup

Scipion installation

For testing this plugin, we need to use the “pluginization version” of Scipion. For that, just install Scipion from GitHub, using the ‘devel-pluginization’ branch. Follow this instructions: https://github.com/I2PC/scipion/wiki/How-to-Install-Scipion-from-sources#from-github

Topaz integration

The following steps presuppose that you have Anaconda or Miniconda installed on your computer.
STEP1:
In ~/.config/scipion/scipion.conf:
Set CONDA_ACTIVATION_CMD variable in the Packages section.
For example: CONDA_ACTIVATION_CMD = . ~/anaconda2/etc/profile.d/conda.sh
Notice the command starts with a period! This will source the conda.sh script. This is needed to activate the conda environment.
For further information please visit the following website:
Set TOPAZ_ACTIVATION_CMD variable in the Packages section.
For example: TOPAZ_ACTIVATION_CMD = conda activate topaz
This will activate the conda environment with the default name topaz.
STEP2:
Type ./scipion installp -p topaz or you can also install it from the plugin manager (1, launch scipion; 2, go to configuration; 3, select plugins). This will conda install topaz for you.
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