Segments volumetric file from a simple threshold which can be set automatically from the otsu estimation.

Usage: volSegment [input] [output]

Allowed options are :

Positionals:
  1 TEXT:FILE REQUIRED                  volumetric input file (.vol, .pgm, .pgm3d, .longvol)
  2 TEXT:FILE REQUIRED                  volumetric output file (.vol, .pgm, .pgm3d, .longvol)
 
Options:
  -h,--help                             Print this help message and exit.
  -i,--input TEXT:FILE REQUIRED         volumetric input file (.vol, .pgm, .pgm3d, .longvol)
  -o,--output TEXT=result.vol           volumetric output file (.vol, .pgm, .pgm3d, .longvol)
  --labelBackground                     option to define a label to regions associated to object background.
  -m,--thresholdMin INT=0               min threshold (if not given the max threshold is computed with Otsu algorithm).
  -M,--thresholdMax INT=255             max threshold

Example:

You can test the segmentation in the lobster volume file:

$ volSegment ${DGtal}/examples/samples/lobster.vol segmentation.vol -m 70 -M 255

DGtal

Definition: ATu0v1.h:57

You will obtain a volumetric file representing for each voxel a label associated to a connected component. You can display this segmentation results by extracting it in SDP format with the vol2sdp tool (with option -e to export also the image labels):

$ vol2sdp segmentation.vol segmentation.sdp -e -m 1 -M 255

and display them with 3DSDPViewer :

$ 3dSDPViewer segmentation.sdp --importColorLabels

You should obtain such a result:

Segmentation result displayed with colors representing the segmentation labels.

See also: volSegment.cpp