Xmipp

xmipp_micrograph_scissor (v3.0)

Usage

Extract particles from a micrograph

See also
micrograph_mark

Parameters

General Options

-i, --untilted <input_untilted_micrograph>
From which the untilted images will be cutted
--orig <original_micrograph>
unless this parameter is specified
--oroot, --untiltfn <oroot>
Name for the particle images Two files will be created: oroot.stk with the particles in a Spider stack an oroot.xmd with the list of image names, the micrograph they were taken from, and their coordinates
--pos, --untiltPos <position_file>
file with particle coordinates

Processing Options

--Xdim <window_X_dim>
In pixels
--downsampling <float=1.>
The positions were determined with this downsampling rate
--Ydim <window_Y_dim>
If not given Ydim=Xdim
--invert
Invert contrast
--log
Take logarithm (compute transmitance)
--appendToStack
The output stack is deleted. Use this option to add the new images to the stack

Options for tilt pairs

-t, --tilted <input_tilted_micrograph>
From which the tilted images will be cutted
--tiltfn <output_stack> ( requires --untiltfn )
Name for tilted images (Stack FileName)
--tiltAngles <angles_file> ( requires --tiltfn )
Name of the estimated tilt angles Angle from the Y axis to the tilt axis. Both (tilted and untilted) must be cut with its corresponding angle. Cut images are rotated so that the tilt axis is parallel to Y axis.
--tiltPos <position_file> ( requires --tiltfn )
file with particle coordinates

Examples and notes

   xmipp_micrograph_scissor -i g7107.raw --pos g7107.raw.Common.pos --oroot images --Xdim 64
   xmipp_micrograph_scissor --untilted Preprocessing/untilt/down1_untilt.raw --tilted Preprocessing/tilt/down1_tilt.raw --untiltfn untilt --tiltfn tilt --Xdim 60 --tiltAngles ParticlePicking/down1_untilt.raw.angles.txt --pos ParticlePicking/down1_untilt.raw.Common.pos --tiltPos ParticlePicking/down1_untilt.raw.tilted.Common.pos

User's comments

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