Image processing for cryo electron microscopy

1 – 11 September 2015 | London, United Kingdom


About the Practical Course

  • Structural analysis by cryo EM has become a major tool for studying large macromolecular complexes. The use of field emission gun microscopes, imaging of samples at liquid nitrogen temperatures, direct electron detectors and developments in image processing have led to improvements in the resolution of single particle structures from 20-30 Å to the atomic level. More complex processing is required to extract the higher resolution details. Cryo EM single particle analysis is an ideal complement to X-ray crystallography and NMR. Fitting of individual structures into cryo EM maps of large assemblies allows the characterization of multi-component interactions, to distinguish different functional states. This hybrid approach is essential for understanding biological mechanisms and is an important addition to structural genomics. New approaches developed for analysis of thin cells and cryo-sections or lamellae by tomography extend the range of EM from individual complexes to cellular structures in situ.

    The aim of the EMBO Practical Course is to teach the basic principles and practical aspects of image processing to bioscientists and structural biologists wishing to determine macromolecular structures by cryo electron microscopy (EM). The practical course will concentrate on processing of single particle images, and will be aimed at advanced PhD students and postdocs using cryo EM images for structural analysis.

    The various specimen types (e.g. individual protein molecules, helical assemblies or large complexes) require different approaches for image analysis and 3D reconstruction. On our EMBO Practical Course we will review the major techniques used in electron microscopy: analysis of single particles and ordered assemblies, electron tomography and sub-tomogram averaging. This will help students in choosing the most appropriate approaches for their own research. However, the major emphasis will be on processing of single particle images.

    The EMBO Practical Course will cover:
  • Basic concepts of Fourier analysis
  • Principles of TEM image formation and contrast transfer
  • Image acquisition and pre-processing
  • Contrast transfer function correction
  • Symmetry and alignment
  • Statistical analysis of images
  • Determination of orientations for 3D reconstruction
  • Methods of 3D reconstruction
  • Tomography and subtomogram averaging
  • Icosahedral reconstruction
  • Refinement and validation of 3D EM reconstructions
  • Interpretation: Atomic structure fitting into EM maps
  • Developments in biological electron microscopy: automated data collection
  • Data deposition






Registration deadline

11 May 2015

Selected participants will be notified by

26 May 2015

Payment deadline

15 June 2015


Academic Industry




Online application

Apply now!




Applications are invited from PhD students and researchers in EM.
Applications should include: a CV; a publication list; a short description of your current work and future plans; an explanation of why attendance at the course would further the applicant's own research. Please upload this in a single PDF in the 'CV Upload' section.
We will also require a reference letter from your supervisor.



Accepted participants will receive a payment link.

Registration includes:

  • Accommodation
  • Meals
  • Course materials and
  • Group excursion.

Does not include travel to and from the venue or extra nights of accommodation before or after the course.


Travel grants

A limited number of travel grants are available for eligible participants. Applicants do not need to apply separately for travel grants for this event. Selection of awardees is handled directly by the organizer who will notify all eligible participants. More information is available at EMBO Travel Grants' page.


Poster specifications

  • Please bring one printed copy of your poster; A0 size, portrait format.
  • Posters should have a border of a few centimetres to allow for the frame.
  • An accompanying presentation; approximately 10-15 mins to explain the poster. This should be PowerPoint (on a USB stick or uploaded to the internet ready for download)


Additional information

  • We will endeavor to put students up in single rooms but due to availability we may have to ask them to share. Bathrooms will be shared with a few other students.




Tim Hoe

+44 020 7631 6849






Birkbeck, University of London

Malet Street, Bloomsbury
London WC1E 7HX

United Kingdom


The Birkbeck electron microscopy (EM) laboratory is one of major international centres for cryo EM and image processing in Europe, with four group leaders covering experimental and computational aspects of macromolecular structure determination by EM. The environment also includes many other leading structural biologists with a strong interest in the EM field.

The college has excellent facilities for lectures and computer based practicals. Lectures will take place in a well-equipped seminar room. There is a meeting room for round table discussion and lunches immediately adjacent to the lecture room. For the practicals we will use a large computer teaching room with 40 networked workstations that provide access to all the necessary software.

Students will have the opportunity to see demonstrations in our cryo EM lab, which has 4 cryo microscopes, including a 300 kV Polara capable of high resolution single particle and tomography data collection, as well as equipment for cell preparation, cryo sectioning and correlative fluorescence and cryo EM.


venue map


Birkbeck College is in central London, with access via four international airports and is well connected to rail/coach/bus services.

  • The nearest Underground station is Russell Square which can be reached directly from Heathrow airport using Piccadilly Line.
  • The nearest mainline railway stations are King’s Cross or Euston. However, all the major stations are served well by the Underground.
  • There are many buses come through the Bloomsbury area of London; checking the Transport for London website would be recommended.