Difference between revisions of "Copenhagen Workshop on Cryo Electron Tomography 2024"
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| − | | Talk || 09:00 - 10:00|| Presentation: Segmentation | + | | Talk || 09:00 - 10:00|| Presentation: Segmentation (Ricardo Riguetto) |
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| 1 || 10:00 - 10:30|| General introduction: Hands on | | 1 || 10:00 - 10:30|| General introduction: Hands on | ||
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| -- || 10:30 - 10:50 || Coffe break | | -- || 10:30 - 10:50 || Coffe break | ||
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| + | | Talk || 10:50 - 11:45|| Presentation: Segmentation II (Ricardo Riguetto) | ||
|- | |- | ||
| 5a || 11:45 - 12:30 || [[Walkthrough on manual marker clicking (SciLifeLab 2023)| Alignment of tilt series: Manual]] | | 5a || 11:45 - 12:30 || [[Walkthrough on manual marker clicking (SciLifeLab 2023)| Alignment of tilt series: Manual]] | ||
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| 5c || 14:15 - 15:00 ||[[Walkthrough_on_command_line_based_tilt_series_alignment (SciLifeLab 2023)| Alignment of tilt series: command line]] | | 5c || 14:15 - 15:00 ||[[Walkthrough_on_command_line_based_tilt_series_alignment (SciLifeLab 2023)| Alignment of tilt series: command line]] | ||
|- | |- | ||
| − | | 6 || 15: | + | | -- || 15:00 - 15:20 || Coffe break |
| + | |- | ||
| + | | 6 || 15:20 - 16:15 || [[Walkthrough on PCA through the command line (SciLifeLab 2023)| Principal Component Analysis ]] | ||
|- | |- | ||
| FHV || 16:15 - 17:30 || [[Complete walkthrough on FHV virus (SciLifeLab 2023)| Complete walkthrough on FHV virus]] | | FHV || 16:15 - 17:30 || [[Complete walkthrough on FHV virus (SciLifeLab 2023)| Complete walkthrough on FHV virus]] | ||
Revision as of 18:10, 23 November 2023
Contents
Workshop
This workshop will take place from January the 24th to January the 27th 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 four-day course.
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 will be updated here prior to the workshop.
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: Denoising in cryo electron tomography (Ricardo Riguetto) |
| -- | 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 Riguetto) |
| 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 |
| Module | Time | Subject |
|---|---|---|
| 4 | 9:15 - 10:30 | Template Matching |
| -- | 10:30 - 10:50 | Coffe break |
| Talk | 10:50 - 11:45 | Presentation: Segmentation II (Ricardo Riguetto) |
| 5a | 11:45 - 12:30 | Alignment of tilt series: Manual |
| Module | Time | Subject |
|---|---|---|
| 5b | 13:30 - 14:15 | Alignment of tilt series: GUI |
| 5c | 14:15 - 15:00 | Alignment of tilt series: command line |
| -- | 15:00 - 15:20 | Coffe break |
| 6 | 15:20 - 16:15 | Principal Component Analysis |
| FHV | 16:15 - 17:30 | Complete walkthrough on FHV virus |
| HIV1 light | 17:30 - 18:00 | Spherical geometry: multiple liposomes |
