Lecture notes


Useful documents


TEM for training part a

TEM operating instructions

TEM note page

Negative staining protocol

cryo-sample preparation using vitrobot

Useful links


  • TEM information without too much math.

  • TEM information with simulations.

  • Chimera is one of the best visualization software.

  • Relion is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). It uses maximum-likelihood classification.

  • EMAN is a software to reconstruct 3D structure based on EM images. The contact is Steve Ludtke at Baylor College of Medicine.

  • Frealign is a software to reconstruct 3D structure based on EM images. The contact is Nikolaus Grigorieff at Brandeis University.

  • XMIPP is a software to reconstruct 3D structure based on EM images. It uses maximum-likelihood classification.

  • Spider is a software to reconstruct 3D structure based on EM images. It is developed and maintained at Wadsworth center in NY.
  • Imagic is a software to reconstruct 3D structure based on EM images.

  • Sparx is a software to reconstruct 3D structure based on EM images. It relies on the EMAN2 library. The contact is Pawel Penczek in the Department of Biochemistry and Molecular Biology at the University of Texas - Houston Medical School.

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