Micrograph_scissor_v3
Extract particles from a micrograph
See also Micrograph_mark_v3
Parameters
General Options $: From which the untilted images will be cutted $: unless this parameter is specified $: 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 $: file with particle coordinates
Processing Options $: In pixels $`--downsampling <float`1.> $: If not given Ydim=Xdim $: Invert contrast $: Take logarithm (compute transmitance) $``: The output stack is deleted. Use this option to add the new images to the stack
Options for tilt pairs $: From which the tilted images will be cutted $ ( requires --untiltfn ): Name for tilted images (StackFileName) $ ( 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. $ ( requires --tiltfn ): file with particle coordinates
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