Leginon Main Page


Leginon is a system designed for automated collection of images from a transmission electron microscope.

Contact information:

leginon issue tracking and repository are moved to

Report bugs and request features at at that site.

Current Release: 3.6

Current Version used at SEMC: Leginon_System_version_beta Newest feature that is used everyday.

Software Installation Manual and User Guide:

Developer Guide:


Primary Publication to Cite:

  • "Automated Molecular Microscopy: The New Leginon System" (2005), C Suloway, J Pulokas, D Fellmann, A Cheng, F Guerra, J Quispe, S Stagg, CS Potter and B Carragher. Journal of Structural Biology 151 (1): pp. 41-60.

Additional References:

  • "Leginon: New features and applications" (2021), Anchi Cheng, Carl Negro, Jessica F Bruhn, William J Rice, Sargis Dallakyan, Edward T Eng, David G Waterman, Clinton S Potter, Bridget Carragher , Protein Sciences 30:pp. 136-150. doi: 10.1002/pro.3967
  • "Rapid, routine structure determination of macromolecular assemblies using electron microscopy: Current progress and remaining challenges", B. Carragher, D. Fellmann, F. Guerra, R.A. Milligan, F. Mouche, J. Pulokas, J. Quispe, C. Suloway, Y. Zhu and C.S. Potter, J. of Synchrotron radiation. 11, pp 83-85 (2004)
  • "A relational database for cryoEM: Experience at one year and 50,000 images", D. Fellmann, J. Pulokas, R.A. Milligan, B. Carragher and C.S. Potter, J. of Structural Biology, 137, p. 273-282 (2002)
  • "Leginon: An automated system for acquisition of images from vitreous ice specimens", B. Carragher, N. Kisseberth, D. Kriegman, R.A. Milligan, C.S. Potter, J. Pulokas and A. Reilein, Journal of Structual Biology 132, 33-45 (2000).
  • "Leginon: A system for fully automated acquisition of 1000 micrographs a day", C.S. Potter, H. Chu, B. Frey, C. Green, N. Kisseberth, T.J. Madden, K.L. Miller, K. Nahrstedt, J. Pulokas, A. Reilein, D. Tcheng, D. Weber and B. Carragher, Ultramicroscopy 77 (1999) 153-161.
  • "Automated cryoEM data acquisition and analysis of 284742 particles of GroEL." (2006) Stagg SM, Lander GC, Pulokas J, Fellmann D, Cheng A, Quispe JD, Mallick SP, Avila RM, Carragher B, Potter CS. J Struct Biol. 155 (3): pp. 470-81. PMID: 16762565.

Software Availability and Licensing Information

Leginon is released under the Apache License, Version 2.0


EM Workshop - Leginon Users Group

Leginon Brainstorm

Updated by Anchi Cheng 3 months ago ยท 41 revisions