DisplayImages

As of release 1.3, RELION has a built-in image display program (called relion_display). It may be launched from the command-line, but more convenient access is offered through the "Display" button on the GUI (which actually launches "relion_display --gui"), which asks the user to select a file for displaying, and then launches a dedicated display GUI.

Display types

There are two main display-types:

• The single-image viewer may be used to visualise individual 2D images, such as individual particle (e.g. with names such as 624@stack.mrcs) or micrographs (e.g. mic001.mrc). In the single-image viewer, left-mouse clicking will print the image value to the terminal, while dragging the middle-mouse can be used to measure distances.

• The multi-image viewer may be used to visualise 3D maps (e.g. run1_it025_class002.mrc) as slices through Z; or stacks of images (e.g. mic001_particles.mrcs); or multiple images that are read from an input STAR file (e.g. run1_it025_data.star). For each image in the multi-image viewer, right-mouse clicking and selecting "show original image" from the pop-up menu will launch the corresponding single-image viewer. Note that the scale of this image can be changed from the original display GUI.

And there are the following specialised display-types:

• The picking viewer is a special version of the single-image viewer, which may be used to manually pick particles from micrographs. Particles are picked with the left-mouse button; and deleted with the middle-mouse button. The right-mouse button launches a pop-up menu that can be used to save a STAR file with the picked coordinates. The rootname of these STAR files may be set on the display GUI.

Display options

There are 3 ways to set the contrast of the displayed images from the display GUI:

1. auto-contrast (sigma-contrast = black-value = white-value = 0) will use a linear greyscale from the lowest value black to the highest value white. This is often useful for displaying particles, slices through 3D maps, or 2D class averages.
2. sigma-contrast will use a linear greyscale from black for the average value minus X times the standard deviation in the image to white for the average value plus X times the standard deviation in the image, where X is the value provided for the sigma-contrast. This is often useful for displaying micrographs.
3. manual contrast will use a linear greyscale between the user-provided values for black and white. This may be useful in special cases, where the auto-contrast or sigma-contrast do not give satisfactory results.

types of files may be displayed:

• individual 2D images (*.mrc) (such as micrographs) individual will be displayed in a matrix-like view (the multiviewer) as slices in Z.

• individual 3D maps (*.mrc) will be displayed in a matrix-like view (the multi-viewer) as slices in Z.

• stacks of images (*.mrcs) will be displayed in the same matrix-like view. Individual images from the stacks can then be displayed separately through clicking the right-mouse pop-up menu on the particle of interest. The same single-image viewer can also be launched from the command-line by providing the individual image name (e.g. 624@stack.mrcs) with the --i option.

 h

Individual maps (with a .mrc extension) will be displayed as slices in Z. All particles in a stack (with a .mrcs extension) will be displayed ni a matrix-like view. Individual images from the stacks can then be displayed through clicking the right-mouse pop-up menu on the particle of interest. If you know which particle to display, you can also provide its name (e.g. 624@stack.mrcs) on the command-line with --i option.