EMBO workshop 2021
These tutorials takes place virtually on the 11th and 13th of September of 2021 (14-18:30), as a part of the EMBO workshop for Image processing in cryoEM
- 1 Tutorials
- 2 Contents
- 2.1 Alignment of tilt series
- 2.2 Models
- 2.3 Template matching
- 2.4 Subtomogram averaging
Please refer to your course material to access your credentials.
Dynamic of the course
The course is divided on different modules, described in the time schedule below. Each module is structured in three stages:
- all students are connected to the main room; goals of the module will be explained by an instructor.
- Individual work
- students go the breakout rooms they have been assigned and perform the tasks of the walkthrough in the tutorial.
- an instructor will be assigned to each breakout room.
- Common discussion
- on the last 5 minutes of the module, we come back to the general breakout room for discussion of problems found.
Each module has one or several walkthroughs. The data of the walkthroughs is sometimes synthetic and created on the fly, and sometimes a data set is necessary. In such cases, the text of walkthrough will point to an on-line location where the data can be downloaded.
During this course, the data will be also available in the filesystem, you will not need to download it.
This time schedule is temptative
Day 1: tomography
|14:30||tilt series alignment: manual|
|15:00||tilt series alignment (GUI)|
|15:30||tilt series alignment (command line)|
|16:30||models: catalogue system|
|17:00||models: helical symmetry|
|17:30||models: vesicles and surfaces|
Day 2: Subtomogram averaging
|14:30||Getting started: synthetic thermosomes|
|15:30||Advanced tutorial: FHV|
|18:00||High resolution pipelines|
Alignment of tilt series
Data location: t.b.d.
Manual alignment of tilt series
We will click manually on the gold beads of our test tilt series Walkthrough on manual marker clicking
Automated alignment of tilt series through the GUI
Automated alignment of tilt series through the command line
Vesicle and surface models
tutorial on membrane modeling with dmslice
Reusing model workflows ( walkthrough)
walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
The data can be found in
Advanced starters guide
from densely packed spherical geometry (~1 hour)
The data is available at
High resolution pipeline
Not a tutorial per se: this is a presentation on a set of tools to interconnect Dynamo, M and other software.