Up: Component summary Component

MorphologyFeatures

Extracts the morphology features from segmented image mask. The component is also a powerfull mask skeletonizer. Note: The table output can be fed to Ellipse2MaskList component.

Example:

SourceOutput
"File"      "Object"  "Area"  "Roundness"  "Eccentricity"  "Ly"    "Lx"    "Alpha"   "Width" "WidthStd"  "Skeleton length" "Distance(1)" "X"  "Y"
"cells.tif"    1       725     0.816384     0.679341        26.075            35.5331        0.0172       23.3238    0            1                95.4365      31.3945          22.1572
"cells.tif"    2       286     0.734701     0.784778        15.3516           24.7696        -0.2169       7.45389  4.27683        25               28.7175      55.0105          234.308

Version 2.2
Bundle anima
Categories Image Analysis
Authors Ville Rantanen (ville.rantanen@helsinki.fi)
Issue tracker View/Report issues
Requires Matlab
Source files component.xml extremaborderlength.m imagemorph.m imagesinglemorph.m skeletonclean.m avgskeletonwidth.m execute.m
Usage Example with default values

Inputs

Name Type Mandatory Description
mask ImageList Mandatory A directory with BW mask image files.
names ImageList Optional A directory with the original image files, for naming the table. If omitted, names from "mask" are used.
masklist MaskList Optional A MaskList source for the objects. If given, the mask input is not used for objects, but must be given for file names.

Outputs

Name Type Description
out CSV List of feature values.
skeleton ImageList Skeletons of the objects. End points are marked with white pixels, branch points with middle gray. Removed points are darker gray (0.4 and 0.9).

Parameters

Name Type Default Description
branchFill float 0 Fill looping branch 'holes' smaller than given value.
branchMin float 0 Shortest accepted branch/end-to-endpoint length.
connectivity int 4 Mask object connectivity. 4 or 8. Does not apply if masklist input is used
nthdist int 1 Value N to calculate the distance to Nth nearest object.
prefix string "" Prefix string for data headers in the result table. Used when reading the same images with multiple parameters and then joining the results.

Test cases

Test case Parameters IN
mask
IN
names
IN
masklist
OUT
out
OUT
skeleton
case1 properties mask (missing) (missing) out skeleton

nthdist=1,
branchMin=15

case2_masklist properties mask (missing) masklist out skeleton

nthdist=1,
branchMin=15


Generated 2018-12-11 07:42:05 by Anduril 2.0.0