EMBO workshop 2021

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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



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.

Data location

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.

The general repository for the data is:


Time schedule

This time schedule is tentative

Day 1: Tomography

Time Subject
14:00 Introduction
14:30 Tilt series alignment: manually
15:00 Tilt series alignment: GUI
15:30 Tilt series alignment: command line
16:00 Break
16:30 Models: catalogue system
17:00 Models: helical symmetry
17:30 Models: vesicles and surfaces
18:00 Template matching

Day 2: Subtomogram averaging

Time Subject
14:00 Introduction
14:30 Getting started: synthetic thermosomes
15:30 Advanced tutorial: FHV
16:00 Break
16:30 FHV: continuation
17:00 Seed oversampling
18:00 High resolution pipelines
18:20 Closing remarks


Alignment of tilt series

We will align the same tilt series tilt series with three different approaches.

The data is available at:


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

Walkthrough on GUI based tilt series alignment

Automated alignment of tilt series through the command line

Walkthrough on command line based tilt series alignment



Helical models


Vesicle and surface models

tutorial on membrane modeling with dmslice

Reusing models

Reusing model workflows ( walkthrough)

Template matching

walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)
The data is available at:


Subtomogram averaging


Guided presentation:

Working on your own:

Basic  walkthrough: creating a catalogue, picking particles, launching a project.

Advanced starters guide

Complete the advanced starters guide (~2 hours) The data can be found in


the chimera path you need in the tutorial is


Seed oversampling

 from densely packed spherical geometry   (~1 hour) 

The data is available at:


High resolution pipelines



Interconnectivity tools

Alister: Not a tutorial per se: this is a presentation on a set of tools to interconnect Dynamo, M and other software.