EMD stands for “Electron Microscopy Dataset.” It is a subset of the open source HDF5 wrapper format. N-dimensional data arrays of any standard type can be stored in an HDF5 file, as well as tags and other metadata. EMD files typically have a “.emd” extension, though they may also have “.h5″ or other extensions. All generic HDF5 file viewers can open EMD files; in addition we provide a viewer for EMD files that allows n-dimensional data to be easily viewed along any combination of axes, as well as integrating along any number of axes. Our viewer can open and convert standard proprietary formats such as Gatan’s digital micrograph “.dm3” datasets and FEI’s STEM “.ser” datasets.
We have developed this format as an open source alternative to the proprietary formats used by commercial hardware and software manufacturers. We chose HDF5 because of its widespread adoption among researchers and easy availability of APIs for many different programming languages. Over time we hope to spur adoption of open source formats in the microscopy community, and the EMD format specifically.