Instruct Course on the development of image processing workflows in streaming and structural data analysis components for Electron Microscopy. Madrid, 2020.


National Center for Biotechnology (CNB), Madrid, Spain
Madrid,  2020
Dates: Postponed until the second half of the year. The final dates will be announced.

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.


Attendees should bring their own laptop with a modern browser.

Medium programming skills are required:

Python skills are desirable.

AWS machines might be provided by us.

Make a list of pre-installed software for Scipion (Linux only, CUDA, OpenMPI etc.) to setup faster during the course

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: Pablo Conesa (PC), Yunior Fonseca (YF), David Maluenda (DM), Laura del Cano (LC), Marta Martínez (MM), Roberto Marabini (RM)

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


1. Scipion installation
2. Pycharm configuration
3. Scipion objects:

a. Mappers (DAO)
b. Scalars
c. Pointers
d. Sets
e. Others

4. Plugin structure – plugin template:

a. Plugin class

i. Variables
ii. Environment
iii. Binaries installation

b. Modules: Protocols, viewers, wizards, objects, bibtex, conf

5. Protocols

a. Class methods: define params, insert steps, steps
b. Folder structure
c. Execution: run.db, steps_parallel vs steps_serial, gpu threads, extra worker thread, streaming, batches

6. Tests
7. Viewers
8. Wizards
9. Projects
10. Create your plugin: practical session to integrate 3rd party software or your own. 


Key dates:

01 – 30 April, 2020: Submission of the course application

01 – 30 April, 2020: Submission of the accommodation grants application

01 – 15 May, 2020: Communication of awarded applications (course and grants)

15  – 31 May, 2020: Payment due



Academic Registration Fee Instruct countries.

Predocs 100 €
Postdocs and Others 150 €

Academic Registration Fee Non Instruct countries

Predoc 150 €
Postdocs and Others 200 €

Industrial Registration Fee 500 €

Fill  your application here. (Registration will be open soon)

Additionally, there are 10 accommodation grants for attendees from Instruct countries

If you want to apply for an accommodation  grant, please send an e-mail to before April 30 including:

  • short CV
  • brief explanation of the impact of this course in your work

This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe.