DM3 Import for Gatan Digital Micrograph
Updated 8 Jan 2013
This script acts to import files from Gatan's .DM3 file format, utilized for electron microscopy, into a MATLAB structure. The fields of the MATLAB structure can then be referenced with the dot-operator.
For example, one can load and display a file with the appropriate scaled axes in nanometers and electrons with the following example script:
dm3struct = DM3Import( 'RandomBrightfieldImage.dm3' );
N = length( dm3struct.image_data );
imagesc( (1:N).*dmstruct.xaxis.scale (1:N).*dmstruct.yaxis.scale, ...
This script currently imports images, EELS spectra, and spectral images. Now imports annotations (text) written on the image as well.
This script was constructed largely by parsing example DM3 files with a hex editor. It uses regular expressions to find the tags that indicate the start points of the various fields within the files, and then strips the data. To the best of my knowledge there is not existing documentation on the actual object used to write DM3 format files so it is not practical to output to DM3 format.
Robert McLeod (2023). DM3 Import for Gatan Digital Micrograph (https://www.mathworks.com/matlabcentral/fileexchange/29351-dm3-import-for-gatan-digital-micrograph), MATLAB Central File Exchange. Retrieved .
MATLAB Release Compatibility
Platform CompatibilityWindows macOS Linux
- Image Processing and Computer Vision > Image Processing Toolbox > Import, Export, and Conversion >
- Sciences > Biological and Health Sciences > Biomedical Imaging >
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Added examples of using DM3Import with a spectral image, and fixed some bugs relating to DM3 files from other instruments.
Added example of using a spectral image and fixed a couple of bugs related to DM3 files from other instruments.
Fixed bugs in the import of spectral images that had an interlacing problem.
Added support for importing microscope state in the form of tags for Hitachi TEMs.
Added support to import annotations written on the screen.
Added support for HAADF images (i.e. datatype '11' in GATAN's scheme) since a user asked for it. If anyone finds other bugs please e-mail me and I will fix them.
Update 02Dec2010: Now with examples, and some changes to import separate xaxis for individual spectra.