Change the range of intensity values of pixels. In general, most of the methods requires a background to separate particles from noise

Parameters

$``: Input file: metadata, stack, volume or image. $--mode <modeoverwrite> where <mode> can be:

• • $--label <image_labelimage> $-o, --output <output_file> $--oroot <root> $--save_metadata_stack <output_md> $: Store the original image filename in the output metadata in column imageOriginal. $: Preserve the columns from the input metadata. Some of the column values can be changed by the program. $``: for 2D-images: do not apply transformation stored in metadata $--method <mthNewXmipp> where <mth> can be:

  • OldXmipp I=(I-m(I))/stddev(I) Avg(I)0, Stddev(I)1, does not need background

  • NewXmipp I=(I-m(bg))/stddev(bg) Avg(bg)0, Stddev(I)1 Positivity constraints can be added in reconstruction

  • I=(I-mean(I))/(stddev(I)*cos(tilt)) does not need background, it assumes the tilt series is vertically aligned Similar toOldXmipp but with an extra division by the cos(tilt)

  • NewXmipp2

  • Subtract ramp and then NewXmipp

  • $: Invert contrast. $`--thr_black_dust <sblack`-3.5> $`--thr_white_dust <swhite`3.5> $`--thr_neigh <value`1.2> $: Requires --method Random. I=aI+b. $: Apply a mask depending on the tilt requires --method Tomography or Tomography0 $:

    where <mode> can be:

• • $ or--mask <mask_typecircular> where <mask_type> can be:
  • $--center <x00> <y0=0> <z0=0>

Normalize using OldXmipp method

xmipp_transform_normalize -i images.sel --method [[OldXmipp]]

Normalize 64x64 images using NewXmipp method

xmipp_transform_normalize -i images.sel --method [[NewXmipp]] --background circle 29

Normalize 64x64 images using NewXmipp method and a crown mask

xmipp_transform_normalize -i images.sel --method [[NewXmipp]] --mask crown 29 32

Normalize a volume to have zero mean and unit variance

xmipp_transform_normalize -i volume.vol --method [[OldXmipp]]

Normalize a volume so that the noise outside a sphere of radius 29 has zero mean and unit variance

xmipp_transform_normalize -i volume.vol --background circle 29