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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

!Show

Purpose

Show is a program that provides a Graphical User Interface for visualization and manipulation of Electron Microscopy Single Particle Images in Spider format. The program can show either a selfile or a volume.

Usage


$ show ...

Parameters

  • `` Show images contained in the selfile
  • `` Show rotational spectra contained in datafile
  • `` Show codevectors (images) in file
  • `` Show codevectors (spectra) in file
  • `` Show classes in thisCL2D analysis
  • `` The volume files to show (if several, separate filenames with spaces). By default, slices are shown along the__Z__ axis, add the lettersx or`y` to the filename to show slices along the__X__ and__Y__ axes respectively. For instance,`some_volume.vol` changes to`some_volume.volx`
  • `` The image files to show (if several, separate filenames with spaces)
  • `` Show a Power Spectrum Density file (these are generated by xmipp_assign_CTF)
  • `` Show a CTF model file (these are generated by xmipp_assign_CTF)
  • `` Show a list of Power Spectrum Density files (these are generated by xmipp_assign_CTF)
  • `` Show a list of CTF model files (these are generated by xmipp_assign_CTF). If you supply the parameters file used for assigning the CTF, then you will be able to recompute any particular CTF simply by right-clicking on the piece you want to recompute. This is the mode for micrograph pieces.
  • `` This is the mode for a list of micrographs where each micrograph has a single CTF.
  • -w [width10] = The width of the grid. 10 by default
  • -h [height10] = The height of the grid. 10 by default
  • `` If the file on disk changes, then change the representation. This option is not valid for selfiles
  • `` The default is to apply the transformation stored in the header of 2D-images. Use this to switch it off
  • `` Use this option to normalize all the volumes or images with the same factors

Examples and notes

Showing Selfiles

If a selection file is selected as described above, the main window with the visualized images appears:

/showsel_main.gif

The window visualizes each individual image and its label.

Controls

Combination Operation
`Ctrl +`__or__`Ctrl P` Double the size of the images
`Ctrl -`__or__`Ctrl M` Half the size of the images
`Spacebar`__or__`Mouse double click` Mark/Unmark individual images
`F1`__or__`Mouse right click` Pop-up menu
By right-clicking on any place in the window area a pop-up menu is shown showing four options:`File`,`Options`,`Help` and`Quit`.

File

The file menu contains two options:Open andSave.

  • Open An open window appears to allow selection of desired sel file.
  • Save Use Save option to save marked images in the sel file in different ways:
    • As discarded Marked images will be saved in the current sel file as discarded (labeled as-1). Xmipp programs will ignore discarded images in their processing. This option is useful when bad images are marked to be eliminated from the population, specially after selecting them from a micrograph.
    • As active and the rest as discarded Marked images will be saved in the current sel file as active (labeled as1) and the rest as discarded (labeled as-1). Xmipp programs will ignore discarded images in their processing. This option is useful when only good images are marked to eliminate the rest from the population, specially after selecting them from a micrograph.
    • In a new sel file The marked images will be saved as active (labeled as1) in a new sel file. The unmarked images will be ignored when saving

Options

TheOptions menu contains important set of operations that can be applied to the whole set of images, mainly for information and visualization purposes:

/showsel_options.gif

The options in the menu are the following:

  • Select All Mark all the images
  • Unselect All Unmark all the images
  • Individual normalization Each image is individually normalized (scaled to the0..255 range) for visualization purposes. This option is set by default
  • Global normalization All the images are normalized (scaled to the0..255 range) according to the minimum and maximum pixel value of the whole set. This option is useful mainly for visualization purposes
  • Show Labels andHide Labels These options allow showing and hiding each image's label
  • Show Image name as labels The name of each image is used as label (default)
  • Show Sel status as labels The status of each image is used as label. The status can be eitherA (Active) orD (Discarded)
  • View Stats This option will take all the marked images and calculate the average and standard deviation Images. The resulting images will show up in a new window:

/showsel_ave.gif

  • Show sel statistics This option will calculate the selfile statistics according to the status of the images (% of active images and percent of discarded images). It is useful to know exactly how many images were discarded by a certain process in Xmipp

Help

Shows important information about this program.

Quit

Close all windows and quit the program

Showing Volumes

If a volume file is selected as described above, the main window with the visualized images appears:

/showvol_main.gif

This window shows the slices of the volume along the Z axis. If you press the left mouse button on some volume point, then the physical coordinate, the logical coordinate and the voxel value at that point is shown on the bottom label. If the-poll option is used, the program will check automatically for file changes. If the file on disk changes, the new volume will be automatically loaded.

An alternative for volume visualization is the program chimera. Xmipp volumes have extension xmp or vol by default. Chimera will recognize them if you modify the file named fileformats.py (located in my computer at /usr/local/chimera/share/VolumeData/) So that the line

('SPIDER volume data', 'spider', ['spider'], ['spi']),

looks like

('SPIDER volume data', 'spider', ['spider'], ['spi','vol','xmp']),

Showing Images

If an image file is selected as described above, the main window with the visualized images appears:

/showimg_main.gif

As shown in the picture, in the status bar at the bottom reflects information about the image. First the "real" pixel coordinates and its real density values are shown(37,4) = 0.586. After that, the real image dimension is shown (in this case70x70) and at the end, within brackets, the actual widget dimension280x280.

By right-clicking on any place in the window area a pop-up menu is shown showing three options:File,Options andHelp

  • File will allow the loading of a new image, saving the current image (Spider and Bitmap image format are supported) and Printing.

/showimg_file.gif

In addition, by left-clicking over the image and moving the mouse, some measures along the image can be carried out:

/showimg_measure.gif

  • Options/Set spacing With this option the spacing of the image can be set. The spacing is given in Angstoms/pixel. The measures given in the image will use this spacing value. By default, the spacing is set to 1

/showimg_help.gif

  • Help will show information about the supported commands:

/showimg_help.gif

--Main.AlfredoSolano - 22 Jan 2007

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