Scipion — A Cryo-EM image processing framework for integration, traceability, and analysis.

Designed for

Software Developers




Structural Biologists


Integration of cryo-EM Software

Scipion integrates existing software allowing you to smoothly switch from one package to another offering countless combinations. Scipion started off with single particle analysis (SPA) methods but the team is currently expanding the toolset to include new features such as atomic modelling and tomography.


Scipion’s strives to provide an entire track of the processing pipeline. New method executions are stored together with selected parameters. All output logs are also stored, allowing the user to analyze the underlying commands and their results.


Scipion users interact through a collection of GUIs that provides a uniform interface for various heterogeneous EM programs. In addition, some parameters have 'wizards' - which are special interfaces that allow the adjustment of parameter values while showing their effects in real time.

Plugin Framework

Scipion is also now a plugin framework. This hastens the release of new packages and new updates, without the need of releasing a new version. Plugins can also install the actual image processing software if the license allows it.


For cryo-EM Facilities

Scipion will processes acquired images on the fly and provides feedback to help make decisions even while the microscope is collecting data.


Multiple options are available to process your data on the fly such as running in batches or multi-GPU jobs handling. Get the most out of your microscope by analyzing results as quick as possible.


Most popular image processing packages like Relion 3, motioncor2, ctffind4, crYOLO, Xmipp, and many more are now integrated. Tomography packages are coming soon.


Most of the steps in SPA analysis in Scipion have several options and is up to YOU to choose them. No Programming skills needed. You can even use several different methods and then apply consensus tools.


Designed to integrate and be integrated. All its functionality can be accessed from any python code (in case you need it) and from version 2.0 it is a plugin-framework.


Monitor your acquisition (drift, gain, ctf resolution, defocus) as well as your system (GPU's, memory, I/O, ...) and define alerts when those values pass a threshold you define.


You can automate all this only a few clicks, Scipion will not bother you unless something goes wrong or you want to have a look at the results.

Workflow Templates

You can define as many workflows as you wish and you can save them as templates. You just need to tell it which workflow to use.


You can apply consensus methods to compare alignments, CTFs and pickings to prune the images providing your users with a "clean" dataset to start the reconstruction.

Live HTML Acquisition Report

You can choose to generate a detailed summary report (in HTML) ready to sync to any public HTTP server, so your external users can follow the data collection progress.

Scipion Plugin Framework in Python

Scipion is a plugin framework ready to discover new EM image processing software once you wrap it as a plugin. Scipion is written in python as are it's plugins too. Python has nowadays gained popularity being one of the most widely used programming language for scientific computing.

Using pypi

Scipion uses to deploy plugins and assures you're in control of your code at any time.

Reach SB Users Fast

Scipion is downloaded 2-3 times a day. You can reach all Scipion users as soon as you publish your plugin.

Automated Testing

Your code, even your binaries, can be regularly tested. Both development and production branches.

Usage Stats

Scipion collecta usage statistics, with user consent, and provides feedback about usage.

Keep Your Methods

There is no need to pack your software with a 3rd party software to create another "full-stack software suite" to cover the whole pipeline.

File Format Conversions

Support of common file formats conversions is provided (mrc, vol, hdf, dm4, mrc4bit, tiff, …). Your software can implement just one and let Scipion/Xmipp do the file format conversion.

Focus on the Method

Scipion provides a uniform GUI. You just need to focus on your protocol implementation and, if desired, create a results viewer.