PSI Workshop 2023

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The PSI Dynamo workshop will take place from August the 16th to August the 18th in the Paul Scherrer Institute.

The workshop provides hands-on training in all practical aspects of tomography and sub-tomogram averaging using our software Dynamo, encompassing all stages of the pipeline: alignment and reconstruction of tilt series, tomogram visualization and archiving, particle selection and extraction, and subtomogram alignment, averaging, refinement and classification. No previous experience is required. Computing infrastructure will be provided in place, and we welcome participants to bring their own data sets to work on them during this four-day course.

Computing resources


Participants will bring their own laptops to access a PSI server which will host the data. However, each participant should also install in their laptop prior to the workshop:

  • (R2023a version), a licence free trial version is available.
  • Dynamo  : prior to installation make sure you have a compiler. On Linux you probably have one by default. On Mac, Xcode needs to be installed. On Windows, the recommended option is to install it via Matlab:


  >> tar -xvf dynamo_temp_1.1.530.tar

Launch the installed package inside MATLAB.

 >> run <DYNAMO_ROOT>/dynamo_activate.m

Wait while some packages are compiled. Activate it again.

Access to PSI resources

This guide describes the steps to follow to access the computing resources inside PSI.

Time Schedule

  • On the third day participants are encouraged to make a flash presentation (3 mins, max. slides) describing their past or planned research in tomography. We will study the particular cases of interest of each participant, and identify tools of possible relevance inside the Dynamo environment, designing with the participants viable processing workflows combining Dynamo and other packages.
Day 1 (Morning) General tools
Module Time Subject
0 09:00 - 10:00 Research Talk
1 10:00 - 10:45 General introduction: Hands-on guide to basic tools.

Basic Dynamo jargon
Basic formats for data and metadata

2 11:00 - 12:30 Starters Guide: subtomogram averaging
3 13:30 - 14:00 General modeling
3a 14:00 - 14:45 Models: Filaments
Additional material: Coordinated extraction from several filaments
3b 14:45 - 15:30 Models: Vesicles
3c 15:30 - 16:30 Models: Surfaces

Day 2 (Morning) General Tools
Module Time Subject
4 09:00 - 10:15 Template Matching
5 10:15 - 11:30 Principal Component Analysis
6a 11:30 - 12:00 Alignment of tilt series: Manual
6b 12:00 - 12:30 Alignment of tilt series: GUI
6c 12:30 - 12:45 Alignment of tilt series: command line

Day 2 (Afternoon): Practical cases
Module Time Subject
FHV 13:30 - 15:30 Complete walkthrough on FHV virus
HIV1 15:45 - 17:00 High Resolution workflow for HIV1: preprocessing

High Resolution workflow for HIV1: Dynamo manipulations
High Resolution workflow for HIV1: binding with Relion

Additional material:


  • Daniel Castano-Diez (CSIC Bilbao, Spain).
  • Raffaele Coray (CSIC Bilbao, Spain).
  • Alma Vivas-Lago (CSIC Bilbao, Spain).