This is a (non-exhaustive) list of freely available software for reading and handling different vendor file formats in electron microscopy.
Feel free to contribute PRs to update the list!
| Format | Vendor | Software | Plugin / Package | Comments |
|---|---|---|---|---|
| tif (TFS/FEI) |
TFS/FEI | ImageJ/Fiji | Bio-Formats Importer, EM tool | Start Bio-Formats Importer from the plugin menu. |
| Python | HyperSpy/RosettaSciIO, imageio, tifffile | tifffile examples: 1,2 | ||
| DigitalMicrograph/GMS | temDM’s “ImportImage” | temDM: Push CTRL while starting the plugin will batch import all images in the folder. | ||
| emi/ser | TFS/FEI | ImageJ/Fiji | TIA Reader, EM tool, CSI | EM tool: Use "TEM .ser .dm3 folder export" to batch convert to scaled TIFF. TIA Reader: Will open multidimensional datasets, e.g. image series/spectrum images (spectra = single 1D "images"). CSI: Use for spectrum images. |
| Python | HyperSpy | |||
| DigitalMicrograph/GMS | temDM’s “ImportImage” | temDM: Push CTRL while starting the plugin will batch import all images in the folder. | ||
| dm3 | Gatan | ImageJ/Fiji | Built-in reader, EM tool, CSI | Built-in reader: No metadata other than image scale (confirm?). EM tool: Use "TEM .ser .dm3 folder export" to batch convert to scaled TIFF. CSI: Use for spectrum images. |
| Python | HyperSpy | A dm3 spectrum file can consist of multiple signals (e.g. fitted components) generated in GMS. | ||
| DigitalMicrograph/GMS | Built-in reader | |||
| dm4 | Gatan | ImageJ/Fiji | Bio-Formats Importer | Start Bio-Formats Importer from the plugin menu. |
| Python | HyperSpy | |||
| DigitalMicrograph/GMS | Built-in reader | |||
| emsa, msa | MSA | NIST-DTSA II | Built-in reader | |
| Python | HyperSpy | |||
| DigitalMicrograph/GMS | Built-in reader | Rename .emsa files to .msa. | ||
| spc* | EDAX | NIST-DTSA II | Built-in reader | |
| Python | HyperSpy | |||
| spd* | EDAX | Python | HyperSpy | |
| spx | Bruker | NIST-DTSA II | Built-in reader | |
| Python | HyperSpy | |||
| bcf | Bruker | Python | HyperSpy | Only EDS data, no EBSD. |
*Not personally tested, only from software documentation.
FEI/TFS microscopes without DigiScan acquire spectrum images (SIs) through the microscope interface (Experiments tab).
DigitalMicrograph offers a nice GUI for processing the data, e.g., NLLS fitting of ELNES features.
To transfer the SI data:
- Load .emi/.ser SI data into HyperSpy
- Save as .rpl/.raw files
- Use ImportRPL plugin to load .rpl/.raw data into DM
A notebook (STEM-SI-Converter) can be downloaded here.