This module computes the error between two segmentations of a volume. The metrics are either based on the Rand Index or Variation of Information, and features a few customizable options. These include:

• Foreground Restriction- computing error over voxels where the second segmentation (presumed to be ground truth) != 0. This is applied as a default option.

• Splitting '0' Segment into Singletons- The segment id of 0 often corresponds to a background segment, however it can also represent singleton voxels after processing by watershed. This option re-splits all segments labelled 0 into new segment ids, recovering the singletons. This is applied as a default option, and disabled by -no_split0

• Boundary Thinning- (not complete yet)

• First Segmentation File (seg1, as .tif file)

• Second Segmentation File (seg2, as .tif file) This should be the "ground truth" segmentation if applicable

• Foreground Restriction (optional flag -nofr, default=on)

• Boundary Thinning (not complete yet)

• Split 0 Segment (optional flag -no_split0, default=on)

• Metric Types (all calculated by default)

• Rand F Score - ISBI 2012 Error Metric

• Rand Error - 1 - RandIndex

• Variation F Score - ISBI 2012 Information Theoretic Error Metric

• Variation of Information

• 2D Metric Types (not calculated by default)

  • Rand F Score -rfs2d
  • Rand Error -re2d
  • Variation F Score -vifs2d
  • Variation of Info -vi2d

make

NOTE: You will see a harmless warning when compiling the Cython functions. See (http://docs.cython.org/src/reference/compilation.html)