Integration of cryo em software

Scipion integrates existing software allowing you to smoothly switch from one package to another offering endless combinations. We started with single particle analysis (SPA) methods but we are currently expanding our toolset to include atomic modelling and tomography. The following graph is dynamic and clickable, you can play with it!

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One of Scipion’s main goals is to provide an entire track of the processing pipeline. Each new method execution is stored, together with selected parameters. All output logs are also stored, allowing the expert user to inspect more deeply the underlying commands and their results. You will always know what have you done!.


Users interact with Scipion through a collection of GUIs that provides a uniform interface for a plethora of heterogeneous EM programs. Also, some parameters have “wizards” - special interfaces that allow the adjustment of parameter values while showing their effects in real time.

Plugin framework

Scipion is now a plugin framework. This will speed up the release of new packages or new updates through a plugin manager, without the need of releasing a new Scipion version. Plugins can also install the actual image processing software "behind", if the license allows it.