Scipion Integration

Its one of the main purposes of SPARTAN to extract and process SMLM single particle data for 3D reconstruction using established software routines from electron microscopy (EM). As SPARTAN generates particle montages, it is compatible with a wide range of different 3D reconstruction programs. We decided to use Scipion since it is a free GUI-based software package that includes already many established EM reconstruction programs such as xmipp, eman, spider or relion.

Since Scipion is only available for Linux systems, we decided to include and provide it as a platform-independent docker package that can be called from SPARTAN on any computer running Matlab and Docker. We successfully tested the interface on Linux and Mac and are currently working on a solution for Windows systems.

Select Volume > Scipion from the SPARTAN menu.

There are three options to interact with Scipion.

1. Go to Scipion opens the project manager to access saved Scipion projects or create new ones.
2. New Single Color Analysis opens a new window where the user can select a particle montage as well as a new project name.
3. New Paired Analysis opens a new window where the user can select two particle montages (i.e. for reference and protein of interest) as well as a new project name.

For options 2 and 3, Start Scipion will generate a new pre-configured Scipion project accordingly and load the standard workflow for a single or dual-color reconstruction.