EMBO workshop 2019

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This page describes the contents of the practical hands-on sessions for tomography through Dynamo at the Birkbeck College during the EMBO School for Image processing in Cryo Electron Microscopy (September 2019).

Installing Dynamo on your laptops

Workstations are provided by the organization. These instructions are intended for those students that want to install their own Dynamoversion in their laptops.


The Dynamo versions on the three platforms can be obtained in the Downloads page. Please use the indications here to install it in your laptop.

Starting a Dynamo session

You need to run an activation shell (see below for information on how to do it on each platform) that can be used to run alignment projects or to initiate an interactive session using the Dynamo console. For this, you can just type:


on a Dynamo-activated system shell and be patient: the first time a shell initiates a Dynamo process, it can takes several minutes. New invocations to the MCR libraries will be much faster, and commands inside the opened Dynamo session will run immediately.


On a Linux terminal, type:

 source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh


On a Mac termina, type:

 source <DYNAMO_ROOT>/dynamo_activate_mac_with_shippedMRC.sh


In a DOS terminal write:

C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat 

then open a Dynamo terminal by typing in the DOS


If it doesn't work, type:

 set PATH=%PATH%;%MCR_ROOT%\runtime\win64

and then again

C:\ <path to the Dynamo installation>\dynamo_activate_windows.bat

Running a Dynamo project in the standalone

When working with the standalone, it is not convenient to run projects directly pressing [Run] in the dcp GUI. It is a better approach to run the project in a different process.

  • Open a new system shell (DOS shell in windows).
  • Activate Dynamo in that shell. i.e.,
    • Linux: source <DYNAMO_ROOT>/dynamo_activate_linux_with_shippedMRC.sh
  • Do NOT start a Dynamo session, i.e., do not type dynamo in the shell.
  • In the terminal, type the name of the execution script.
    • Linux/Mac: ./ptest.exe
    • Windows: ./ptest.bat


Before the hands-on session, we will go to this presentation for a general introduction of the Dynamosoftware.

In the room

Clicking particles in the Starters guide

Guided presentation:

Working on your own

Use of the command line

    • tutorial on the use command line operations for general purposes.
    • tutorial on the use of the command line to manage projects.

Geometric modeling

Geometric modeling for surfaces and filaments

Short guided presentation:

Template matching

Working on your own:

  • We will follow this walkthrough for automated identification of proteosomes on a real tomogram through template matching. (~1 hour)

Adaptive bandpass filtering

Working on your own:

  • We will follow this walkthrough to create a small synthetic data set that illustrates the principles of adaptive bandpass filtering, a way of conducting a golden standard alignment procedure . (~40 mins)


Short guided presentation:

Creation of 3D scenes

Working on your own:

Further support material.

  • Walkthrough on depiction and manipulation of triangulations (synthetic data).

Additional tools

Wednesday afternoon session.

Data sets

The data sets will be updated here.


  • Daniel Castaño-Díez, University of Basel.
  • Giulia Zanetti, Birkbeck College.