Göttingen Workshop 2024

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This workshop will take place from April the 10 to April the 12th 2024 in the European Neuroscience Institute (ENI), Room 2.006.

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-days course.

Computing resources


For the first two days, participants will bring their own laptops . However, each participant should also install in their laptop prior to the workshop:

  • (R2024a 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_1.1.532.tar

Launch the installed package inside MATLAB.

 >> run <DYNAMO_ROOT>/dynamo_activate.m

Wait while some packages are compiled. Activate it again.

Workshop data

The data that will be used during the workshop can be downloaded using the google drive link: https://drive.google.com/drive/folders/10lZjjKj1tMfVL_RYJioaK12ji3_RdrNT?usp=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 https://drive.google.com/drive/folders/1EXXGPMQZhD0lKurzaQ6Nz0Vypj3WUkJP?usp=drive_link (750MB)
Alignment of tilt series https://drive.google.com/drive/folders/1VPYk91xJ6cLCSy6Mg4UX_dDLHHIhhbp9?usp=drive_link (600MB)
Virus like particles https://drive.google.com/drive/folders/1Vr108rtKI7knFOmzL06-nfFm1KCKdq4e?usp=drive_link (4.6GB)
Spherical geometries https://drive.google.com/drive/folders/1arrd1KcscsvCDEasmNISShujWjWCYjlw?usp=drive_link (64 MB)
Principal Component Analysis Data generated locally by Dynamo
Complete walkthrough on FHV virus https://drive.google.com/drive/folders/10j1mGTV-4srVV2Hg98eWkAPhPeAbU5BQ?usp=drive_link (2GB)
Walkthrough on hexagonal lattice coherence through neighborhood analysis https://drive.google.com/drive/folders/1jberboXIRNp32GvZ14XV_6N2R-tnYESD

Access to computational resources

On the third day, a more advanced tutorial will be completed. For this we will to access a server which will host the data. Access details will be updated here.

Time Schedule

  • On the third day participants are encouraged to make a flash presentation (3 mins, max. 2 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 09:30 - 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 General Tools
Module Time Subject
4 09:30 - 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
Neigh 13:30 - 14:00 Neighborhood analysis
FHV 14:00- 17:00 FHV
Day 3 (Whole day): Practical case: High resolution workflow.
Module Time Subject
HIV1-Introduction 9:30 - 10:00 HIV1 presentation:https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing
HIV1-0 10:00 - 10:20

High Resolution workflow for HIV1: Overall view

HIV1-a 10:20 - 10:50 Preprocessing (presentation)
HIV1-ai 10:40 - 11:20 Preprocessing (individual work)
HIV1-ap 11:20 - 11:30 Preprocessing (Discussionn)
HIV1-b 11:30 - 11:45 Dynamo manipulations (presentation)
HIV1-b 11:45 - 12:30 Dynamo manipulations (individual work)
Lunch 12:30 - 13:30 Lunch
HIV1-b 13:30 - 13:45 Dynamo manipulations (discussion)
HIV1-c 13:45 - 16:45 Refinement and binding with Relion
agur 16:45 - 17:00 Final remarks

Additional material:


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