xmipp_transform_threshold (v3.0)


Threshold volumes and images

See also
transform_mask transform_morphology


-i, --input <input_file>
Input file: metadata, stack, volume or image.
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
--label <image_label=image>
Label to be used to read/write images.
-o, --output <output_file=>
Output file: metadata, stack, volume or image.
--oroot <root=>
Rootname of output individual images. Output image format can be set adding extension after rootname as ":ext".
--select <mode>
Select pixels meeting
where <mode> can be:
  • abs_below <th> Absolute value below a threshold
  • below <th> Below a threshold
  • above <th> Above a threshold
--substitute <substitutionMode=value>
Substitute selected pixels by
where <substitutionMode> can be:
  • binarize Selected are set to 0, non-selected to 1
  • value <new=0> New value
  • noise <avg=0> <stddev=1> Gaussian noise
  • avg Average of non-selected

Examples and notes

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

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