Scipion for facilities
'scipion-em-facilities' plugin allows to use different utils for cryo-EM facilities (like monitors) within the Scipion framework.
Monitors are used to produce live analysis plots, generate reports or raise alerts when some problems are detected. A monitor example is the CTF-monitor, that checks the computed defocus values for each micrograph as they are generated. CTF-monitor may raise an alert if the defocus values are above or below certain thresholds. A special case of this monitors is the monitor summary which encapsulates the CTF Monitor, the system monitor and the movie gain monitor and continuously creates a report.
This module contains protocols and utilities related with monitors.
Please, check the facilities documentation for more details.
You will need to use Scipion 3.0 to be able to run these protocols. If you want to use the summary monitor with grafana you will need to create the file secrets.cfg in the directory defined by the variable EMFACILITIES_HOME (see the above mention web site for details).
To install the plugin, you have two options:
- Stable version
scipion3 installp -p scipion-em-facilities
- 1st. Download repository
git clone https://github.com/scipion-em/scipion-em-facilities.git /path/to/scipion-em-facilities
- 2nd. Install the plugin
scipion3 installp -p /path/to/scipion-em-facilities --devel
To check the installation, simply run the following Scipion test:
scipion3 test --grep emfacilities --mode modules --run
--run is not passed, it only shows the available tests to check.