Open TEM, STEM and SEM files without the microscope software
Electron microscopes save their pictures and spectra in formats that only the vendor software
opens: Velox .emd, DigitalMicrograph .dm3/.dm4, TIA .ser, Bruker .bcf and others. When
the licence lives on the microscope computer, getting a figure for a paper or the raw numbers for
your own analysis means going back to the lab. This converter reads the files directly and gives
you pictures with a correct scale bar, calibrated TIFFs for ImageJ and Fiji, EDS maps, spectra as
CSV and every acquisition setting stored in the file.
What it reads
| Instrument software | Files | What is converted |
|---|---|---|
| Thermo Fisher (FEI) Velox | .emd (file versions 4 to 13) | HAADF, BF, DF, DPC, iDPC, camera and diffraction images, frame series and drift-corrected stacks, FFTs, EDS spectra, EDS spectrum images (the raw event stream of every detector), EELS spectrum images, the element maps saved by Velox |
| Gatan DigitalMicrograph | .dm3, .dm4 | images and stacks in every number type (8 to 64-bit, float, complex, packed FFT, RGB), diffraction patterns, EELS, EDS and CL spectra, line scans and spectrum images |
| FEI / Thermo Fisher TIA | .emi with its .ser files | images, image series, diffraction patterns, EDS spectra, line scans, spectrum images, diffraction scans |
| Berkeley EMD | .emd, .h5 (NCEM, ncempy, Prismatic, py4DSTEM) | images, stacks, spectra, spectrum images, 4D-STEM data |
| SEM, FIB and camera TIFFs | .tif from Thermo Fisher/FEI (Quanta, Helios, Scios, Apreo...), Zeiss SmartSEM, TESCAN (with or without the .hdr file), Hitachi and JEOL (with their .txt file, also .bmp and .jpg), JEOL SightX, Zeiss ORION, Fibics, TVIPS, ImageJ and DigitalMicrograph | the picture, its pixel size, the instrument settings and the info bar |
| Bruker Esprit | .bcf, .spx | EDS hypermaps (every packing variant, with the element list, the SEM/STEM images and the overview image), single spectra |
| Oxford Instruments AZtec | .h5oina | electron images, EDS element maps with their AZtec colours, per-pixel spectra, the layered image |
| EDAX (Genesis, TEAM, APEX) | .spd with .spc and .ipr, .spc, .lsd | spectrum maps, line scans, spectra |
| JEOL Analysis Station | .img, .map, .pts, .eds | electron images, element maps, spectrum maps, spectra |
| Other | .mrc (with a Direct Electron info.txt), Quantum Detectors .mib, Phenom .elid, EMSA .msa | images, stacks, 4D-STEM scans, Phenom projects with their spectra and maps, spectra |
Upload several files at once, or a .zip of a folder; files that belong together (an .emi and
its .ser files, a picture and its .txt or .hdr) are matched by name.
What you get
- Pictures with a scale bar as PNG or JPEG. The bar has a round length (200 nm, 2 µm, 5 1/nm for diffraction) taken from the pixel size in the file, in the corner and colour you choose. Stacks give the average of all frames, the first frame or every frame.
- Calibrated TIFF for ImageJ and Fiji: the original values (8 and 16-bit as recorded, other types as 32-bit float) with the pixel size and unit, so Analyze, Set Scale already shows the right numbers. Stacks are one multi-page TIFF.
- Info bar removed. The strip with the instrument settings at the bottom of SEM pictures is cut off before the scale bar is drawn: its height comes from the metadata for Thermo Fisher/FEI and TESCAN files and is found in the picture for Zeiss, Hitachi and JEOL.
- Spectra as CSV (energy and counts, all detectors and their sum) with a chart preview.
- Spectrum images: the sum spectrum, a total-counts map, one map per element and a colour overlay, the maps as a TIFF stack, and the whole data cube (y, x, energy, with calibrated axes) as a Berkeley EMD (HDF5) file that ncempy, HyperSpy and other HDF5 software open.
- 4D-STEM: the mean diffraction pattern and virtual bright-field and annular dark-field images instead of thousands of patterns.
- Metadata as readable text and as JSON: accelerating voltage, magnification, pixel size, detector, dwell time, working distance, stage position, date and every other entry in the file.
Element maps
Velox and AZtec files often contain the element maps their software calculated; these are used
as they are. For other spectrum images the maps are made from the elements stored in the file
(Velox, Bruker and EDAX keep a list) or the ones you type, for example Fe, Ni, O or Au M.
Each map counts the X-rays in an energy window around the element's main line (K below about
10 keV, otherwise L or M) that is twice the typical peak width of an EDS detector at that energy
(130 eV at Mn Kα). This is a qualitative map: there is no background subtraction, peak
deconvolution or quantification, so overlapping lines show up in both maps. The pictures are lightly smoothed (3 × 3 pixels, adjustable); the TIFF
and CSV files keep the raw counts.
How accurate is it?
The pixel sizes, energy calibrations and decoded data of the test files (pictures, stacks, spectra and spectrum images) were compared value for value with RosettaSciIO, the open-source reader behind HyperSpy, for every format it reads, and agree. For Velox spectrum images the spectrum summed from the decoded X-ray events also matches the sum spectrum Velox stores in the file.
Privacy
Files are processed on our server only to make your downloads, and the results are deleted automatically after 30 minutes. Operator and sample names, comments and other settings stored inside your files never go into our statistics.
Not supported yet
Velox files saved as "reduced data" lack the raw EDS stream; their pictures, maps and spectra are converted but the spectrum image itself is not. Raw-mode Merlin frames, EBSD orientation data, Delmic cathodoluminescence files and Phenom files from before Element Identification 3.8 are not read. Quantification (weight or atomic percent) is not calculated.