[3dem] Announcing Scipion 1.0

Jose Maria Carazo carazo at cnb.csic.es
Wed Feb 24 06:05:44 PST 2016

Dear EM-community,

We are proud to announce the release of Scipion v1.0.0

(http://scipion.cnb.csic.es), our software workflow framework to obtain 3D

of macromolecular complexes that integrates multiple EM software packages.

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


Installation instructions can be found at:


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

1. Integration and Interoperability

Scipion 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

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 Reproducibility

All 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 template

is a text file that can be easily shared (email, http, etc)

3. Graphical tools

Scipion 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 API

All 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

to operate with images and metadata files.

5. Extensibility

Scipion 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.

Any feedback is welcome.

Scipion Development Team

Prof. Jose-Maria Carazo
Biocomputing Unit, Head, CNB-CSIC
Spanish National Center for Biotechnology
Darwin 3, Universidad Autonoma de Madrid
28049 Madrid, Spain

Cell: +34639197980
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