Converting dm3 Files into Other Formats

Digital Micrograph files (dm3 files) use a proprietary format from Gatan that contains a huge amount of useful meta-data from the microscope and the CCD camera (information such as magnification, exposure length, a recording timestamp, pixel size, etc.). Unfortunately, this format is not easy to display using commonly available image display software. However, it is possible to convert dm3 files into formats that can be more easily displayed in several different ways:

This list of conversion programs and scripts is not meant to be exhaustive, and other software packages installed on Karst may have programs that can convert dm3 files into formats that are more useful for image processing.

Note: Many image format conversion programs numerically alter the original image data and can result in the loss of information. For example, the dm3 files saved by the 3200FS are stored as signed 32-bit integers (even though the CCD camera only produces 16-bit data), and starting from the same dm3 image, DM will save TIFF images that are unsigned 8-bit, unsigned 16-bit or signed 32-bit integers. DM can also save the same signed 32-bit dm3 images as compressed 24-bit JPEG images (an RGB image with 8 bits/channel) or an MRC image stored as 8-bit integers (MRC mode 0). All of these conversions made by DM alter the images numerically either by losing bit-depth (conversion to 8- or 24-bit images) or by adding a constant to each pixel in the image (16-bit TIFF images). Such numerical alterations are undesirable when further image processing is planned, and as mentioned above, it is best to convert dm3 files into MRC files using proc2d.