scipion-em-smartscope 3.0.0

Installation

You will need to install SmartScope previous the plugin installation https://docs.smartscope.org/ Follow the steps to install it with Docker https://docs.smartscope.org/installation.html (Installation with Anaconda/Miniconda is not abailable yet)

Developer’s version

• download repository

git clone -b devel https://github.com/scipion-em/scipion-em-smartscope.git

• install

scipion installp -p /path/to/scipion-em-smartscope --devel

• Smartscope provide a token when the installation finish and you are logged, visit https://docs.smartscope.org/api/rest/prog_api/#obtaining-an-api-token for more details. Please add the token in the scipion.conf file as SMARTSCOPE_TOKEN = …XXXfeb270a1bc4120b1XXXX…

• Smartscope will save the data (not the acquisition managed by SerialEM) in the path you decided in the installation procedure https://docs.smartscope.org/getting_started/installation/docker/docker/#1-download-the-minimal-configuration-files. Please, provide that information on the scipion.conf as SMARTSCOPE_DATA_SESSION_PATH = path/smartscope/save/data

• Add the url to acces to the Smartscope web, by default is http://localhost:48000/ but if you change the url or the port please add the new url in the scipion.conf as SMARTSCOPE_LOCALHOST = http://localhost:48000/

Once you edit the scipion.conf please save it and run scipion config

Protocols

• smartscope connection

• Provide calculations

• Smartscope feedback