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Scipion v1.0.0 Release


We are proud to announce the release of Scipion v1.0.0 (, our software workflow framework to obtain 3D maps of macromolecular complexes that integrates multiple EM software packages.

Scipion is open-source software and can be freely downloaded from: instructions can be found at:

Scipion's main features (while we wait for the paper describing it to be out) are:

1. Integration and InteroperabilityScipion transparently integrates several software packages such as: Xmipp, Relion, Spider, Eman, Sparx, Frealign and Ctffind, among others.The system allows users to easily combine different programs in the same project in the form of a graphical workflow. All required format conversions are done automatically. More than 100 protocols are currently implemented, see the full list at:

2. Traceability and ReproducibilityAll parameters used and steps performed are stored! The entire workflow is presented as a workflow tree or as a list. Several steps can be copied and re-executed with different parameters. The workflow, or part of it, can be exported to a template that can imported into a different project. The workflow templateis a text file that can be easily shared (email, http, etc)

3. Graphical toolsScipion comes with several built-in graphical tools. All protocols are executed from a form that contains validations and help messages for each parameter. A data viewer is provided that can visualize images, volumes, micrographs and their related metadata (shifts, angles, weights, etc). The data viewer is very useful for sets manipulation, also stored as steps in the project history.

4. Automation and APIAll the operations that can be done from the GUI can also be done from Python scripts. This includes creating a new project, launching runs and repeating previous runs, among others. Developers also have Python libraries to operate with images and metadata files.

5. ExtensibilityScipion is designed with extensibility in mind. As a result, new algorithms and visualization tools can be added with relative small effort. Everyone is welcome to contribute.

A good starting point is the tutorials page:

During this year we will have multiple Scipion workshops. Do not miss your next one at:

We hope Scipion will be a useful tool for the whole community, for novice as well as experienced users.

I2PC Scipion Development Team