Copenhagen Workshop on Cryo Electron Tomography 2024
Contents
Workshop
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
Laptops
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:
https://es.mathworks.com/help/matlab/matlab_external/install-mingw-support-package.html
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/dynamo_activate_linux_shipped_MCR.sh
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: 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 | 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) |
Time Schedule
- On the first day we will present the basic tools in the Dynamo environment.
- The second day will be devoted to a hands-on guide on two practical cases:
- Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package Navarro PP, Stahlberg H and Castaño-Díez D (2018). Front. Mol. Biosci. 5:82.
- Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo Scaramuzza S, Castaño-Díez D (2021). PLoS biology. 19(8):e3001318.
- 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.
| 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 |
| 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 |
| 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 |
| 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 |
| 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. |
