Auto3DEM is a semi-automated image reconstruction system that provides all the tools to process raw micrographs acquired at an electron microscope and generate a three-dimensional reconstruction. The most intensive computational procedure like orientation search and reconstruction can be executed either in serial or in parallel on a computer cluster. A graphical interface, RobEM, is also provided both for image processing and visualization purposes.

Download software



A tutorial is provided, along with a data set, to get familiar with the software. The tutorial explains all the procedure to go from digitized micrographs to a 3D reconstruction.

P22 small data set (Requires auto3dem_v4.03 or later)


If you encounter any problem with Auto3DEM or if you have any question, please use the AUTO3DEM forum. The archives of the forum are free to access, while you need to register to post a message.


If you use this software, please cite:

Yan X., R. S. Sinkovits, and T. S. Baker (2007) AUTO3DEM - an automated and high throughput program for image reconstruction of icosahedral particles. J. Struct. Bio. 157:73-82. (pdf)

If you generate an initial model using the Random Model Computation method, please also cite:

Yan X., K. A. Dryden, J. Tang, and T. S. Baker (2007) Ab initio random model method facilitates 3D reconstruction of icosahedral particles. J. Struct. Bio. 157:211-225. (pdf)


AUTO3DEM is free to use for educational, research and non-profit purposes (see LICENSE).


Auto3DEM is currently partially funded by NIH Grant R01-GM033050.
Previous funding: NIH R01-GM087708 (2010-2014).


The software is the result of the cumulative development of many people over the last 30 years. Here is a hopefully exhaustive list of those who have contributed:

Robert Ashmore, Tim Baker, David Belnap, Giovanni Cardone, Holland Cheng, James Conway, Steve Fuller, Yongchang Ji, Hong Lin, Robert Lynch, Dan Marinescu, Eric Meyer, Norm Olson, Robert Sinkovits, Jinghua Tang, Benes Trus, Michael Unser, Xiaodong Yan, Wei Zhang, Xing Zhang