Leginon

h1. Leginon Main Page

h2. Overview

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

h2. Contact information:

h1. leginon issue tracking and repository are moved to https://github.com/leginon-org/leginon.

Report bugs and request features at https://github.com/leginon-org/leginon/issues at that site.

h2. Current Release: 3.7 https://github.com/leginon-org/leginon/releases/tag/myami-3.7.1

h2. Current Version used at SEMC: [[Leginon_System_version_beta]] currently sync with myami-3.7

h2. python3 version (myami-python3 branch) that will be released as 4.0 is in the work at https://github.com/leginon-org/leginon

h2. Software Installation Manual and User Guide:

h2. With End-of-Life on CentOS 7, our autoinstallor no longer works since it could not find the needed downloads.  If you still want an easy installation, please use the docker image made for tutorial purpose and then change the myami version within it.  If you have good solution, please let us know.

* To learn all the details, start with "An introduction to Leginon":/redmine/projects/leginon/wiki/An_introduction_to_Leginon

* To install Leginon, see "Getting Started as a System Administrator":/redmine/projects/leginon/wiki/Getting_Started_as_a_System_Administrator

* To learn how to use Leginon for everyday work, see "Getting Started as a basic Leginon user":/redmine/projects/leginon/wiki/Getting_Started_as_a_basic_Leginon_user

* "Full Leginon Manual Table of Contents":/redmine/projects/leginon/wiki/Leginon_Manual

h2. Developer Guide:

* [[Leginon Developer Guide]]

h2. Publications:

h3. 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.

h3. 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.

h2. Software Availability and Licensing Information

Leginon is released under the "Apache License, Version 2.0":http://www.apache.org/licenses/LICENSE-2.0

h2. Miscellaneous

[[EM Workshop - Leginon Users Group]]

[[Leginon Brainstorm]]