scipion-em-topaz 3.0

Topaz ready to use in scipion.

Topaz plugin

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.

Setup

For Users

Install Scipion3, follow the ‘Topaz integration’ instructions below and install the Topaz plugin.

For developers

1. 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.

2. Follow the ‘Topaz integration’ instructions below.

3. Clone this repository in you system:

   cd
   git clone https://github.com/scipion-em/scipion-em-topaz

4. Install the Topaz plugin in devel mode:

   scipion installp -p ~/scipion-em-topaz --devel

Topaz integration

The following steps assume that you have Anaconda or Miniconda installed on your computer.

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:

https://github.com/conda/conda/blob/master/CHANGELOG.md#440-2017-12-20

Set TOPAZ_ENV_ACTIVATION variable in the Packages section.

For example: TOPAZ_ENV_ACTIVATION = conda activate topaz-0.2.3

This will activate the conda environment with the default name.