Metadata-Version: 1.0
Name: scipion-em-topaz
Version: 3.0.1
Summary: Topaz ready to use in scipion.
Home-page: https://github.com/scipion-em/scipion-em-topaz
Author: I2PC
Author-email: scipion@cnb.csic.es
License: UNKNOWN
Description: 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.
        
        
        .. _Topaz: https://github.com/tbepler/topaz
        
        .. _Scipion3: https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html
        
        .. _install: https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#step-4-installing-xmipp3-and-other-em-plugins
        
        .. _GitHub: https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#from-github
        
Keywords: scipion cryoem imageprocessing scipion-3.0
Platform: UNKNOWN
