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

micrograph_mark

Purpose

This utility allows you to mark and cut micrographs as well as to generate a list of coordinates with the positions to cut. The program admit single or tilted couples of micrographs (markpair mode). The operation manual is as follows:

  • Click with the mouse left button on the overview in order to select the part of the micrograph you desire

  • Use Ctrl-+ and Ctrl-- in the overview window to Zoom-in and Zoom-out respectively

  • Use Ctrl-G to adjust the contrast (min, max and gamma) of the image

  • Use Ctrl-S to save the particle coordinates. If you are marking a tilt pair, you must press Ctrl-S on both images

  • Use Ctrl-R to change the radius of the circle that "marks" each selected particle. NOTE: if you are working in tilted mode left and right windows have independent radius

  • Mark particles with the mouse left button on the micrograph window

  • If you are in MarkPair mode, select particles in the untilted image, the corresponding point will be drawn in the tilted micrograph. If you don't like the position of the automatically generated particle you can move by clicking with the left mouse button

  • Click with the mouse right button over a selected particle in order to remove it or move it

  • You can select several families of particles within the same micrograph. A dialog window tells you which are the possible families (you can add a family in that window). When you select a particle it belongs to the highlighted family

  • You can load a set of particle coordinates in the highlighted family, the new coordinates are appended to the old ones in that family. When you save the particle coordinates, they are saved in a file called as the micrograph, plus the family name, plus the extension .pos. For instance, tilt.raw.Common.pos. It is important that this convention is used since the family name ("Common") is used to match paired pictures

  • When loading particles in two micrographs (tilting pairs) the conversion matrix (the one which passes coordinates from one micrograph to the other) is not computed. For computing it, click on "Save angles"

  • "Save angles" is an option for paired micrographs which computes the tilting angle of the tilted micrograph, and the angle from the Y axis to the tilt axis (clockwise angles are positive) for both images. The result is written in a file called as the untilted image with the extension ".ang"

  • When cutting the micrograph into particles you can choose a different file from which to cut. This is used if you want to mark on a downsampled image and cut from the original one. You must supply the root name for the particles and the window size. This window size will be applied directly without any scaling to the micrograph to be cut. Te popup window that appear after selecting the option "generate images" will allow you to invert contrast and compute optical density from transmitance data

  • You can apply filters to the image being visualized, so that you can see particles better. Filters are added into a queue, so whenever you change the visualized area, they are applied again. Select the menu filter in the overview and add so many filters as you like. You can clean the filter queue, if you want to return to the original image

  • After cutting all images you can use Mask to apply the mask you prefer and Normalize to normalize the set of images

  • IMPORTANT: when working in markpair mode you the tilt and untilted image are independent. For example: if you save the position of the particles in the untilted window you are not saving it in the tilted (by the way, be sure to provide two DIFFERENT file names for the tilt and untilted positions)

Usage


$ micrograph_mark -i [image]
</Verbatim>

*Parameters*
   * =%BLUE% -i [image] %ENDCOLOR%= Input file
   * =%GREEN% -tilted [tilted image] %ENDCOLOR%=
   * =%GREEN% -reverse_endian %ENDCOLOR%=
   * =%GREEN% -auto [Model rootname] %ENDCOLOR%=
   * =%GREEN% -autoSelect %ENDCOLOR%=

You can supply a single image or an image and its tilted version. In case that it is a 16-bit raw file you can reverse the endian status of the file while reading. Watch out that for any input file there must exist a .inf file (for instance for tilt.raw the correspondign .inf file is named tilt.raw.inf) with the following structure:

<verbatim>
# Bits per sample
bitspersample= 8
# Samples per pixel
samplesperpixel= 1
# Image width
Xdim= 2000
# Image length
Ydim= 3000
# offset in bytes (Optional, zero by default)
offset= 0
# Is a signed or Unsigned int (Optional, by default true)
is_signed = true

This file is usually created by convet_tiff2raw.

The only exception is when the input data is an SPIDER file, then no extra information is needed.

Examples and notes

  • Notice that image which have been downsampled from an 8-bits raw image are usually 16-bits raw images
  • If the size of the original image is not a multiple of the downsampling factor, then you will experience problems when marking particles in the downsampled image and cutting from the original. The particles will be moved by [xstep]*([Xdim] mod [xstep]). See micrograph_window for a solution.
  • To convert Web coordinates to Mark coordenates (when using a single micrograph NOT a pair) you may use /web_to_mark.shThis

Mark a single image which has been downsampled:


$ micrograph_mark -i untilt.downsample.raw

Mark a couple of images image which have been downsampled


$ micrograph_mark -i untilt.downsample.raw -tilted tilt.downsample.raw

Automatically select particles in a micrograph


$ micrograph_mark -i micrograph.raw -auto Model -autoSelect

-- Main.AlfredoSolano - 16 Jan 2007

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