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Viewing Digital Micrograph DM3 files

Digital Micrograph Save Screen

Where do I find image parameters like microscope magnification and pixel size?
The DM3 file format is the gold standard for saving Digital Micrograph files. The metadata in the image stores microscope and image information that is lost if the image is stored in any other format type. However, programs such as Adobe Photoshop do not, natively, read the DM3 files so that means users are forced to go to machines where the Digital Micrograph program is installed.

One solution is to use the "Save Display As.." option and then save the image as a tiff or some other format. We have set the default with this option to save full-resolution images rather than as low-res, screen captures. Doing this, however, does not save the metadata.

A good option is to use the free program ImageJ. It has a built in feature that recognizes the DM3 format. Alternatively, for older versions of ImageJ a reader plugin that reads the DM3 file format is available. ImageJ has the standard image enhancement features that are found in most programs but it also has the ability to calculate FFTs which makes the program especially valuable to microscopists. Plugins are also available for a wide range of functions. Another nice feature about ImageJ is that it is available in all of the major OS platforms. It is produced by the Research Services Branch of the NIH.

If you want to save the DM3 files as tiffs in ImageJ you have to do one more step. Go up to Image/Type and change that to either 8 bit or 16 bit. Photoshop cannot properly read the 32 bit file. Then save the file as a tiff in the File/Save As menu option.

Another option is to use the progam EMAN which is a suite of programs for calculating single particle reconstructions from EM images. EMAN is available from the National Center for Macromolecular Imaging.

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