EMD stands for “Electron Microscopy Dataset.”

EMD is a living standard. The current version is EMD 1.0.  The emdfile Python package writes EMD 1.0 specified HDF5 files, and reads v1.0 as well as v0.1 files.  See also the 0.1 spec and 0.1 viewer.

EMD 1.0 is both a specification and a format.  The current standard implementation of EMD 1.0 is using the HDF5 file format.  We chose HDF5 for our standard implementation because of its widespread use in scientific computing and the availability of APIs for many different programming languages.

EMD is intended to clarify, simplify, and facilitate storing and sharing of scientific data through an open format flexible enough to store any possible type of electron microscopy data.  With these tools we aim to encourage sharing, collaboration, and open science in the microscopy community.  If you have questions or comments, please contact us.

Velox EMD & Berkeley EMD

Unfortunately, there are two formats called “EMD” being used in electron microscopy today. The format discussed here was defined at the National Center for Electron Microscopy, part of The Molecular Foundry at Lawrence Berkeley Laboratory, in 2012. The other EMD was defined by the FEI company, now a part of ThermoFisher Scientific, as part of their Velox software used in transmission electron microscopy data acquisition and analysis. Both EMD formats are built on the open HDF5 standard which can be read with various free and open tools. If you need help with Velox EMD, we recommend contacting ThermoFisher. If you’re unsure which kind of HDF5 file you have, try checking the top-level tags.