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Sphire ready to use in scipion.

Project description

=====================
Sphire scipion plugin
=====================

Plugin to use Sphire programs within the Scipion framework

So far we have implemented:

- crYOLO Version 1.2.2

=====
Setup
=====

- **Please follow installation instructions from**:
`Sphire webpage <http://sphire.mpg.de/wiki/doku.php?id=downloads:cryolo_1&redirect=1>`_ in order to install:
- crYOLO (last tested version: 1.2.2)
- crYOLO's boxmanager (last tested version: 1.1.0).

- **If you want to use the generic model**, please download also the General
PhosaursNet model and edit the ~/.config/scipion/scipion.conf file in such a way that exists the following

.. code-block::

CRYOLO_GEN_MODEL = path/to/the/downloaded/General_PhosaursNet_model


- **Install scipion-em-sphire as a Scipion plugin**


.. code-block::

scipion installp -p scipion-em-sphire

OR

- through the plugin manager GUI by launching Scipion and following **Configuration** >> **Plugins**

Alternatively, in devel mode:

.. code-block::

scipion installp -p local/path/to/scipion-em-sphire --devel

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