Displaying dm3 Files

Direct Display of dm3 Files

A screenshot of the EMAN1 software using the v2 display program to examine a dm3 image.

Digital Micrograph files (dm3 files) can be displayed directly using a few programs in addition to Digital Mirograph (DM). If you are connecting to Karst from another Unix/Linux machine or from a Mac (or have an X server like Hummingbird's Exceed or Xming running on a Windows PC), you can use the display programs v2 or boxer from the EMAN1 package to examine dm3 images:

$ v2 image_file
$ boxer another_image_file
examples:
$ v2 image.dm3
$ boxer image.dm3
$ v2 image1.dm3 image2.png image3.mrc image4.pif

NOTE: v2 can be used to display multiple files from a single command-line invocation. Both v2 and boxer can be used to display a number of different file formats (dm3, png, mrc, jpg, pif, etc.)

A screenshot of the EMAN1 software using the boxer display program to examine a dm3 image.

Both these programs allow the user to modify the display parameters by opening a dialog window using the middle button on a 3-button mouse. Once this window has been opened, the display can be adjusted by using the "B" (brightness) and "C" (contrast) sliders (or by typing values into the text box beside each slider). You can change the apparent magnification of the displayed image by entering values into the "scale" text box to the right of the sliders. This modifies the magnification of the displayed image but not the size of the display window itself. The size of the display window can be altered boxer from EMAN1by using the mouse pointer and left mouse button to grab and drag an edge or corner of the window to make it larger or smaller. If the display window is too small to show the full image at the chosen magnification, you can drag the image around using the right mouse button. This is somewhat easier when using boxer since you also have a separate window that shows the displayed area as an outline within the boundary of the full image at the right side of the main boxer control window. The area displayed in this window can be dragged using the left mouse button and causes appropriate changes to happen in the display window itself. In addition, boxer opens another window (labeled "Image View") that is initially blank (solid black in most cases) but that can be used to display boxed out sub-regions of the displayed image.

A screenshot of the proc2d program functioning using the bshow Linux command.

Another program available on Karst that will allow you to display dm3 files directly is the program "bshow" which is part of the Bsoft suite of programs. This program is started by typing

$ bshow
$ bshow single_image_file
examples:
$ bshow
$ bshow myImage.dm3
$ bshow anotherImage.jpg

NOTE: You cannot open multiple files using a single command line invocation of bshow. As with the EMAN1 programs, bshow can also be used with a very large number of file formats.

The "autoscale" button at the bottom of this window sets the Min and Max displayed values to produce a nice display. You can open a second window that allows you to zoom into this image by clicking on "Window/Magnify" in the toolbar across the top.

This program has many other functions.

Read descriptions on other imaging functions offered by bshow

Remember that you may need to connect to Karst using "ssh -X username@karst.uits.iu.edu" in order to have the X-display from these programs forwarded properly to your computer.

A screenshot of the ImageJ program being used to "Show info" on dm3 files.

You can also use ImageJ to display dm3 files using any computer that supports ImageJ (including Karst, where you can start the program by typing "imageJ" on the command line). One of the advantages of using ImageJ to imageJ and a displayed imagedisplay dm3 files is that all the meta-data present in the dm3 images imageJ dropdown menu(pixel size, magnification, when the image was recorded, etc.) can be accessed using the "Image/Show Info..." dropdown menu. This opens up a new window that contains all the metadata.

View an example of the metadata contained within Digital Micrograph files

A screenshot of the ImageJ program being used to display dm3 files.

It will be necessary to familiarize yourself with the organization of this rather user-unfriendly display of that information. However, all the information is available and this is the only way to access that information without using Digital Micrograph to display the file.

NOTE: Different display programs will display these images using different parameters and color schemes. For example, DM automatically ignores the brightest and darkest values in each image (using a "percentage-to-ignore" that the user can control) while v2 and boxer use the full dynamic range (and almost always need manual adjustment of "brightness" and "contrast" before the displayed images look "good" - click the middle mouse button of a 3-button mouse and adjust the sliders labeled "B" and "C"). Also, it is important to understand the co-ordinate system that is used by any given display program. For example, v2 and boxer display images using the lower left corner as the (0,0) location while DM and imageJ display images using the upper left corner as the (0,0) location.

Displaying dm3 Files

Direct Display of dm3 Files

Electron Microscopy Center resources