Copenhagen Workshop on Cryo Electron Tomography 2024

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This workshop will take place from January the 24th to January the 26th in Copenhagen.

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 three-day course.

Flash talks

The attendees will present their work in a short flash talk during the workshop.

Computing resources


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

  • Matlab (R2023a version), 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:

Access to Amazon resources

The information on how to access the amazon session will be given during the workshop.

Dynamo has been installed on the desktop in the folder dynamo_tests. The Dynamo standalone version without GPUs will be used in this workshop.
The workshop data (see next section) has been downloaded in the desktop folder workshop_data. The data for each module has been saved in separated subfolders.

Once connected, you can activate Dynamo by opening a terminal and running: cd Desktop and source dynamo_tests/
Once Dynamo is activated, you can open the Dynamo standalone by running the command: dynamo

It is possible that there may be some rescaling issues with the Dynamo GUI when connecting remotely to the Amazon session. To reduce these effects, it is best to access the session from a maximised browser window.

Workshop data

The data that will be used during the workshop can be downloaded using the google drive link:

In detail, the data for the respective modules is as follows (for a total of about 8GB):

Module and data source
Module Data source
Starters Guide: subtomogram averaging Data generated locally by Dynamo
Models: Filaments Data generated locally by Dynamo
Models: Vesicles Data generated locally by Dynamo
Models: Surfaces Data generated locally by Dynamo
Template Matching (750MB)
Alignment of tilt series (600MB)
Virus like particles (4.6GB)
Spherical geometries (64 MB)
Principal Component Analysis Data generated locally by Dynamo
Complete walkthrough on FHV virus (2GB)

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, 24.01.23 (Afternoon): Presentations
Module Time Subject
Talk 14:00 - 14:50 Presentation: Dynamo
Talk 14:50 - 15:30 Presentation: markerless alignment tomography (Ricardo Righetto)
-- 15:30 - 15:50 Coffe break
Flash 15:50 - 18:00 Flash talks from participants
-- 19:00 Course dinner

Day 2 25.01.23 (Morning) General tools
Module Time Subject
Talk 09:00 - 10:00 Presentation: Segmentation (Ricardo Righetto)
1 10:00 - 10:30 General introduction: Hands on
-- 10:30 - 10:50 Coffe break
2 11:00 - 12:30 Starters Guide: subtomogram averaging

Day 2, 25.01.23 (Afternoon): Modelling
Module Time Subject
3 13:30 - 14:00 General modelling
3a 14:00 - 14:30 Models: Filaments
Additional material: Coordinated extraction from several filaments
3b 14:30 - 14:45 Models: Vesicles
3c 14:45 - 15:00 Models: Surfaces
-- 15:00 - 15:20 Coffe break
HIV1 light 15:20 - 18:00 Virus like particles or Spherical geometries or Spherical geometry: multiple liposomes

Day 3 26.01.23 (Morning) General Tools
Module Time Subject
Talk 9:20 - 10:00 Presentation: Segmentation II (Ricardo Righetto)
4 10:00 - 10:45 Template Matching
-- 10:45 - 11:15 Coffe break
5a 11:15 - 11:45 Alignment of tilt series: Manual
5b 11:45 - 12:30 Alignment of tilt series: GUI
Day 3 26.01.23 (Afternoon): Practical cases
Module Time Subject
5c 13:30 - 14:00 Alignment of tilt series: command line
6 14:00 - 15:00 Principal Component Analysis
-- 15:00 - 15:20 Coffe break
FHV 15:20 - 17:00 Complete walkthrough on FHV virus
-- 17:00 - 17:15 Closing remarks.