DisplayImages

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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. The right-mouse menu also gives access to functionalities to calculate average and standard deviation images from selected images, or to save a STAR file with only the selected images.

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. This viewer is the only one that can low-pass filter the input image internally before displaying it (as this is often useful for picking in micrographs). If you would like to display any other low-pass filtered image, use the relion_image_handler program to low-pass filter the image before displaying. By default, picked particles are shown with green circles, but a blue<>red colour scale may also be used to colour particles based on any numerical value in the input coordinate STAR file (e.g. rlnAutopickFigureOfMerit or rlnClassNumber), or in a second input file. An example of the latter may be a data.star file from a final refinement, where particles are coloured for example based on rlnClassNumber. Any particles in that data.star file will be coloured from red->blue, while particles not in that STAR file will be coloured green. This may be useful in order to understand which particles on the micrographs actually make it into the final refinement.
  • The classes viewer is a special version of the multi-image viewer, which may be used to visualise the results from 2D or 3D classification runs. It is loaded when selecting a _model.star file from the initial file selector. It will look for the model_classes table in the input STAR file and displaying the rlnReferenceImage(s) stored in there. The speciality of this viewer lies in the right-mouse pop-up menu, which may be used to launch a new window with the individual particles in the selected classes, or save the particles from the selected classes in a new particles.star file. Thereby, using "awk" commands for this task, as advocated for older versions of RELION is no longer necessary. :-)

Display options

STAR files

The single-viewer and the multi-viewer may be used directly to visualise individual micrographs, maps or particle stacks. However, the display program may also directly read STAR files, which is extremely useful because:

  1. Upon reading a STAR file, the display GUI will recognise any metadata-label that represents an image that can de displayed (i.e. rlnImageName (default), rlnReferenceImage, rlnCtfImage or rlnMicrographName), and present you with a drop-down menu to choose which images to display.
  2. The metadata on the same line for each image is stored inside the display program (try "Print metadata" from the right-mouse pop-up menu on top of an image in the multi-viewer). This allows you to sort the images in the display based on any numerical value in the STAR file! By default the sorting is from low at the top to high at the bottom. Use the "reverse sort?" option on the GUI for the opposite order.
  3. If the STAR file contains orientational parameters (rlnAnglePsi, rlnOriginX, rlnOriginY) those may be applied to the images, so they will be "aligned" in the display.


Useful examples

  • After running the particle sorting program, a column called rlnParticleSelectZScore is added to the input particles.star. Sorting the images from low-Z at the top (i.e. nice particles) to high-Z at the bottom (i.e. bad particles) is useful to clean-up your data set relatively quickly. The right-mouse pop-up menu options to select all images above or below the current one, or to invert the current selection make this task more convenient. The same pop-up menu may be used to save the selected particles in a new STAR file.
  • After running CTFFIND3 on all micrographs, one can quickly examine the power spectra and the estimated models by displaying the output STAR file, choosing the rlnCtfImage (not the rlnMicrographName!!). Ordering these images on rlnCtfFigureOfMerit helps to quickly identify badly modelled CTFs.
  • Sorting class averages (in the special classes viewer) on rlnClassDistribution (reversed) or rlnAccuracyRotations is helpful to select your best classes.

Contrast

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

  1. auto-contrast (set 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.

Read whole stacks?

The display program has an option to speed-up reading STAR files with (almost) all particles from large stacks. By default, the display program will open and close the corresponding stack for each line in a STAR file. By providing the --read_whole_stack option, entire stacks are read into memory and therefore only opened and closed once. This becomes less helpful once fewer particles from each stack are actually inside the STAR file. Therefore, in practice one probably would not use this option very often.

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