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.

Time schedule

This time schedule is temptative

Day 1: tomography

day 'time
14:00 Introduction
14:30 tilt series alignment: manual
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

Data location: t.b.d.

Manual alignment of tilt series

We will click manually on the gold beads of our test tilt series

Automated alignment of tilt series through the GUI

Automated alignment of tilt series through the command line



Helical models

Vesicle and surface models

Reusing models

Template matching

Subtomogram averaging


Advanced starters guide

Seed oversampling

High resolution pipeline

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