Up: Component summary
Up: Component summary
Component
MorphologyFeaturesExtracts 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:
| Source | Output |
|---|---|
 |  |
"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, |
||||||
| case2_masklist | properties | mask | (missing) | masklist | out | skeleton |
|
nthdist=1, |
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