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        "description": "Topaz plugin\n============\n\nThis plugin allows to use Topaz programs within the Scipion framework.\nIt will allow to pre-process micrographs and pick particles within\nScipion.\n\n`Topaz`_ is a pipeline for particle detection in cryo-electron\nmicroscopy images which uses convolutional neural networks trained from\npositive and unlabeled examples.\n\nSetup\n=====\n\nFor Users\n---------\n\nInstall `Scipion2`_, follow the 'Topaz integration' instructions below and `install`_ the Topaz plugin.\n\nFor developers\n--------------\n\n1. For testing and develop this plugin, you need to use the Scipion v2.0 in devel. \n   For that, just install Scipion from `GitHub`_, using the \u2018devel\u2019 branch. \n2. Follow the 'Topaz integration' instructions below.\n3. Clone this repository in you system: \n   ::\n\n      cd\n      git clone https://github.com/scipion-em/scipion-em-topaz\n   \n4. Install the Topaz plugin in devel mode:\n   ::\n      \n      scipion installp -p ~/scipion-em-topaz --devel\n\n\nTopaz integration\n-----------------\n\nThe following steps presuppose that you have Anaconda or Miniconda installed on your computer.  \n\n| In ``~/.config/scipion/scipion.conf``: \n| Set CONDA_ACTIVATION_CMD variable in the Packages section.\n| For example: ``CONDA_ACTIVATION_CMD = . ~/anaconda2/etc/profile.d/conda.sh``\n| Notice the command starts with a period! This will source the conda.sh script.\n  This is needed to activate the conda environment.\n| For further information please visit the following website:\n| https://github.com/conda/conda/blob/master/CHANGELOG.md#440-2017-12-20\n| Set TOPAZ_ACTIVATION_CMD variable in the Packages section. \n| For example: ``TOPAZ_ACTIVATION_CMD = conda activate topaz``\n| This will activate the conda environment with the default name topaz.\n\n\n.. _Topaz: https://github.com/tbepler/topaz\n\n.. _Scipion2: https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html\n\n.. _install: https://scipion-em.github.io/docs/release-2.0.0/docs/scipion-modes/install-from-sources#step-4-installing-xmipp3-and-other-em-plugins\n\n.. _GitHub: https://scipion-em.github.io/docs/docs/scipion-modes/install-from-sources#from-github",
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