Instruct-ERIC Events

Instruct Course on the development of image processing workflows in streaming and structural data analysis components for electron microscopy

Registration Date: 01-Sep-2020 to 30-Sep-2020
Date: 26-Oct-2020 to 29-Oct-2020

Contact: Blanca Elena Benitez Silva


Overall aims and course outline

Electron microscopy is a well-established and rapidly growing structural technique. There are some consolidated software packages like Relion, Xmipp, Cistem, Eman, IMOD, TomoJ, … that address the image processing steps required for single particle analysis and electron tomography. There are also independent software tools that address a particular and isolated task like movie alignment, CTF determination, particle picking, etc. Software platforms like Scipion facilitate the integration of packages from many different laboratories, and promote the cross-checking of the results by alternative methods. Additionally, Scipion keeps track of all the operations, parameters and steps undertaken from the raw data to the final maps and models, promoting, in this way, the reproducibility of the results. Scipion is used at individual laboratories and at general cryoEM Facilities worldwide. Scipion is quickly expanding to cover the atomic modelling steps and, more recently, tomography software.

This course will show how to integrate into Scipion any software related to electron microscopy data analysis. You will learn the basic Scipion architecture and to construct a fully functional plugin containing the main elements: protocols, viewers and wizards. The course is aimed at programmers, engineers, computational scientists, physicists, mathematicians, and in general to information technology related scientists with interest in integrating their ideas or software into Scipion. Especially welcome are those developers of software packages or independent software tools for Electron Microscopy. It is suggested that attendees come with their own computer in which they can install software development tools.

Target Audience

Software developers interested in developing a Scipion plugin or integrating their software in Scipion.


Remote course

Medium programming skills are required:

  • Python skills are desirable.
  • AWS machines might be provided by us.

If you want to use your own laptop for development instead of you may need:

  • OS Linux (Ubuntu recommended)
  • CUDA (if you have a GPU)
  • python3
  • Conda or miniconda (optional, otherwise we will use virtualenv)


Lead contact:
Carlos Oscar Sorzano

Pablo Conesa

Administrative Contact:
Blanca Benitez


I2PC staff: Carlos Oscar Sanchez-Sorzano (COSS), David Maluenda (DM), Jorge Jiménez (JJ), Pablo Conesa (PC), Roberto Marabini (RM), Yunior Fonseca (YF).

Other tutors: José Miguel de la Rosa Trevín (JMRT from SciLifeLab in Stockholm), Grigory Sharov (GS from MRC-LMB in Cambridge)

Find the full program here.

Registration opens on 1 September 2020. More information, including how to register, can be found on the I2PC website.

Madrid, Spain

Instruct Course on the development of image processing workflows in streaming and structural data analysis components for electron microscopy