Difference between revisions of "Copenhagen Workshop on Cryo Electron Tomography 2024"

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| Template Matching || https://drive.google.com/drive/folders/1EXXGPMQZhD0lKurzaQ6Nz0Vypj3WUkJP?usp=drive_link
 
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| Alignment of tilt series || 1
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| Alignment of tilt series || https://drive.google.com/drive/folders/1VPYk91xJ6cLCSy6Mg4UX_dDLHHIhhbp9?usp=drive_link
 
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| Complete walkthrough on FHV virus || 1
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| Complete walkthrough on FHV virus || https://drive.google.com/drive/folders/10j1mGTV-4srVV2Hg98eWkAPhPeAbU5BQ?usp=drive_link
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Revision as of 10:27, 19 January 2024

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.


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:

Module and data source
Module Data source
Starters Guide: subtomogram averaging Data generated locally be dynamo
Models: Filaments Data generated locally be dynamo
Models: Vesicles Data generated locally be dynamo
Models: Surfaces Data generated locally be dynamo
Template Matching https://drive.google.com/drive/folders/1EXXGPMQZhD0lKurzaQ6Nz0Vypj3WUkJP?usp=drive_link
Alignment of tilt series https://drive.google.com/drive/folders/1VPYk91xJ6cLCSy6Mg4UX_dDLHHIhhbp9?usp=drive_link
Virus like particles 1
Spherical geometries 1
Principal Component Analysis Data generated locally be dynamo
Complete walkthrough on FHV virus https://drive.google.com/drive/folders/10j1mGTV-4srVV2Hg98eWkAPhPeAbU5BQ?usp=drive_link

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: Denoising in cryo electron 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


Day 3 26.01.23 (Morning) General Tools
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 Righetto)
5a 11:45 - 12:30 Alignment of tilt series: Manual
Day 3 26.01.23 (Afternoon): Practical cases
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
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