Threshold volumes and images

See also Transform_mask_v3 Transform_morphology_v3

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. $``: Select pixels meeting where <mode> can be:
  • $--substitute <substitutionModevalue> where <substitutionMode> can be:

Threshold a volume below a threshold

xmipp_transform_threshold -i volume.vol -o volumeThresholded.vol --select below 0.01 --substitute value 0

Generate a binary mask based on a threshold and apply it

xmipp_transform_threshold -i volume.vol -o mask.vol --select below 0.5 --substitute binarize
xmipp_transform_morphology -i mask.vol --dil
xmipp_transform_mask -i volume.vol -o volumeMasked.vol --mask mask.vol