EMEN2: an object oriented database and electronic lab notebook

Microsc Microanal. 2013 Feb;19(1):1-10. doi: 10.1017/S1431927612014043. Epub 2013 Jan 29.


Transmission electron microscopy and associated methods, such as single particle analysis, two-dimensional crystallography, helical reconstruction, and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biology / methods*
  • Cryoelectron Microscopy / methods
  • Databases, Chemical
  • Electron Microscope Tomography / methods
  • Electronic Data Processing / methods*
  • Internet
  • Software*