Since some files with the dm3 extension are not standard image files (e.g., EELS spectra recorded using DigitalMicrograph), using these commands (scripts) will occasionally create "empty" files when the conversion is not possible. The command line argument "shrink_factor" allows for the output PNG images to be reduced in size by the value set with "shrink_factore" (e.g., the command "dm2png.sh 4" will convert 4098 x 4098 dm3 files into 1024 x1024 PNG files) while the "scale_bar_length" argument controls the length of the scale bar that will be placed in the TIFF images (e.g., the command "dm2tiff.sh 100" will convert dm3 files into TIFF files that have a scale bar of length 100 of whatever units will be most appropriate for a given image, usually nm or µm). These commands will convert all the dm3 files in the current directory into either MRC, PNG or TIFF files. These scripts make use of other programs such as proc2d command from EMAN1 and imageJ from the NIH and their most useful feature is that they allow the user to convert lots of dm3 files using a single command entered on the command line: Among these are several scripts that can be used to convert dm3 images into MRC, PNG or TIFF format. This last command will produce image1.mrc, image2.mrc, image3.mrc and image4.mrc.Īll users on Karst should have access to programs and file manipulation tools that are designed to work with the data collected using the microscope.
$ bconvert -output mrc myImage.dm3 $ bconvert -output mrc *dm3 $ bconvert -output mrc image1.dm3 image2.tif image3.jpg image4.jpeg To convert into MRC format instead of PIF, use the following commands: $ bconvert myImage.dm3 $ bconvert *dm3 $ bconvert image1.dm3 image2.tif image3.jpp image4.jpegĪll these commands will output PIF image files where the name of the output file(s) are identical to the input files except that the file name extension has been replaced by "pif" (e.g., myImage.dm3 becomes myImage.pif). Unlike proc2d, bconvert will convert multiple files using a single command-line innvocation: Both these file formats are useful for further image processing, but remember that some image display programs (e.g., imageJ) will be understand MRC but not PIF file formats. bconvert will convert any of the image formats that Bsoft understands (including dm3 files) into either PIF ("Portable Image Format," the native file format for auto3dem) or MRC files. It is a command-line driven program available on Karst and is similar to proc2d except that it essentially only performs image format conversions. The TIFF format used for batch conversion makes 8-bit integer images and retains a scale bar (but the length is printed using a font that is so small it is nearly invisible).īconvert is a conversion tool from the Bsoft suite of programs. After choosing the file format, click "OK" and every dm3 file in the selected folder (and all sub-folders, if that checkbox is checked) will be converted to the selected format. This will open a window that allows the user to chose a folder and the file format.
Correlated Light and Electron Microscopy.Using Specific Rappture Interfaces on Karst.Documents for the Leica EM AFS 2 Freeze Substitution Robot.Leica EM AFS-2 Freeze Substitution Device.Direct Electron DE-64 Camera Pixel Sizes.Gatan UltraScan 4000 Current Pixel Sizes.Gatan UltraScan 4000 Pixel Sizes Before October 2017.Using Drift Correction with the Gatan OneView Camera.