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        "description": "Sphire Scipion plugin\n=====================\n\nThis plugin allows to use cryolo within Scipion framework.\nSo far we have implemented:\n\n- crYOLO particle picker\n- JANNI denoising\n\nThis plugin is able to install cryolo (which includes janni) and the generic models for both picking\nand denoising.\n\n`crYOLO`_ is a pipeline for particle detection in cryo-electron\nmicroscopy images which is based on the deep learning object detection system \"You Only Look Once\" (YOLO).\n\n`JANNI`_ (Just Another Noise 2 Noise Implementation) implements a neural network denoising tool based on\ndeep learning.\n\nSetup\n=====\n\nIt is assumed that `Scipion3`_ is currently installed. If not, follow the instructions `here`_.\n\nPlugin scipion-em-sphire requires to have Conda (Anaconda or Miniconda) installed and not initialized in\nthe shell.\n\n- **Install this plugin in user mode:**\n\n    It can be installed in user mode via Scipion main window (**Configuration** >\n    **Plugins**) or using the command line:\n\n.. code-block::\n\n    scipion installp -p local/path/to/scipion-em-sphire\n\n- **Install this plugin in developer mode:**\n\n.. code-block::\n\n    scipion installp -p local/path/to/scipion-em-sphire --devel\n\n\nPlugin integration\n------------------\n\nThe following steps presuppose that you have Anaconda or Miniconda installed on\nyour computer.\nIf you don't have the optional SCIPION_HOME/config/scipion.conf create it like this\n\n::\n\n [PYWORKFLOW]\n CONDA_ACTIVATION_CMD = eval \"$(/path/to/conda/bin/conda shell.bash hook)\"\n \n \nThis also should work . /anaconda2/etc/profile.d/conda.sh. Note the conda initialization is tricky with csh shell and might not work.\n \nIf you wish to install the plugin with the default settings just go to plugin\nmanager and install scipion-em-sphire. This will create the default environment\nnamed cryolo-x.x.x (where x.x.x is referred to the downloaded version of cryolo) for you.\n\nYou are ready to use crYOLO and JANNI.\nIf you wish to change the environment name you can introduce\n**CRYOLO_ENV_ACTIVATION** variable in the ``~/.config/scipion.conf`` variables section:\n\nFor example:\n::\n\n CRYOLO_ENV_ACTIVATION = conda activate cryoloenvname\n\n**Note**: If you have a cryolo installation outside of Scipion and you want to use, follow these steps:\n\n    1. Install the plugin without the binaries:\n\n        .. code-block::\n\n            scipion installp -p scipion-em-sphire --noBin\n\n    2. Create a symbolic link to the crYOLO environment following the naming convention \"cryolo-x.x.x\", e.g:\n    \n        .. code-block::\n\n            ln -s <path_of_conda_environment> cryolo-1.8.0 \n    \n\n    3. Edit the **CRYOLO_ENV_ACTIVATION** variable as described above in the config file and rename the environment.\n\n\nDownloaded crYOLO and JANNI general models can be found, respectively, in the following locations:\n\n``<SCIPION_HOME>/software/em/cryolo_model-[model_version]``\n\n``<SCIPION_HOME>/software/em/cryolo_negstain_model-[model_version]``\n\n``<SCIPION_HOME>/software/em/janni_model-[model_version]``\n\nRunning only with CPU\n---------------------\nCrYOLO is able to `run in CPU <http://sphire.mpg.de/wiki/doku.php?id=downloads:cryolo_1&redirect=1#run_it_on_the_cpu>`_, however this is only recomended for predicting task, not trainning. For that reason, the CPU implementation is only enabled for the ``crYOLO-Picking protocol``. In this protocol, both implementation are possible and you must select one of them in the GPU section of the from.\n\nThe CPU implementation of crYOLO **is not installed by default**. Therefore, to be able to run the CPU version of crYOLO-picking, you must install the `cryoloCPU-[version]` package in the ``Plugin Manager >> scipion-em-sphire`` or by running\n\n``scipion3 installb cryoloCPU``\n\nThe CPU integration of crYOLO is installed under a conda environment called ``cryoloCPU-[version]`` . If you want to modify this environ name, please set the following variable in the scipion's config file.\n\n``CRYOLO_ENV_ACTIVATION_CPU = conda activate cryoloCPU-envName``\n\nRunning plugin tests\n--------------------\nTo check that everything is properly installed and configured, you might want\nto run some tests:\n\n.. code-block::\n\n   scipion test --grep sphire --run\n   \n   \n.. _crYOLO: https://cryolo.readthedocs.io/en/latest/\n\n.. _JANNI: https://sphire.mpg.de/wiki/doku.php?id=janni\n\n.. _Scipion3: http://scipion.i2pc.es/\n\n.. _here: https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install.html\n\n.. _install: https://scipion-em.github.io/docs/release-3.0.0/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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