This plugin allows to use Topaz programs within the Scipion framework. It will allow to denoise, pre-process micrographs and pick particles within Scipion.
Topaz is a pipeline for particle detection in cryo-electron microscopy images which uses convolutional neural networks trained from positive and unlabeled examples.
For testing and develop this plugin, you need to use the Scipion v3.0. For that, just install Scipion from GitHub, using the ‘devel’ branch.
Follow the 'Topaz integration' instructions below.
Clone this repository in you system:
cd git clone https://github.com/scipion-em/scipion-em-topaz
Install the Topaz plugin in devel mode:
scipion installp -p ~/scipion-em-topaz --devel
The following steps assume that you have Anaconda or Miniconda installed on your computer.
CONDA_ACTIVATION_CMD = . ~/anaconda2/etc/profile.d/conda.sh
TOPAZ_ENV_ACTIVATION = conda activate topaz-0.2.3