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Morphological 2D/3D Operations

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Description

Morphological Ops

Performs morphological operations on 2D and 3D objects in the Selection layer of the dataset, modifying the layer based on the chosen operation. See MATLAB’s bwmorph, bwmorph3, and bwskel functions for details.

Demonstration
Skeleton for 3D objects

Select the morphological operation from the Morphological operation dropdown.

For applicable operations (e.g., Thin, Skeleton), optionally specify the number of iterations in the Limit to field and choose the processing dimension with the Apply to radio buttons, selecting Current slice or Whole dataset.

Use the 3D objects checkbox to do morphological operations in 3D.

For applicable operations (e.g., Thin, Skeleton), optionally specify the number of iterations in the Limit to field.

Click the Continue button to modify the Selection layer, or use the Cancel button to close the dialog without changes.

List of available morphological operations

Branch Points

branchpoints: finds branch points of the skeleton in 2D or 3D Selection layer objects:

Useful for identifying junctions in skeletal structures, such as in vascular or neuronal networks.

Clean

clean: removes isolated voxels from the 3D Selection layer:

  • 3D processing only.
  • Reference: bwmorph3

Effective for eliminating single-pixel noise in 3D datasets, improving object clarity.

Diagonal Fill

diag: eliminates 8-connectivity of the background using diagonal fill in the Selection layer:

  • 2D processing only (Diag).
  • Reference: bwmorph

Helps refine object boundaries by adjusting connectivity, useful for segmentation tasks.

End Points

endpoints: finds end points of the skeleton in 2D or 3D Selection layer objects:

Ideal for pinpointing termini in skeletal structures, such as tips of branches or fibers.

Fill

fill: fills isolated interior voxels (0s surrounded by 1s in 6-connectivity) in the 3D Selection layer, setting them to 1:

  • 3D processing only.
  • Reference: bwmorph3

Corrects small gaps within 3D objects, enhancing structural continuity.

Majority

majority: keeps a voxel at 1 in the 3D Selection layer if 14 or more voxels in its 3x3x3, 26-connected neighborhood are 1; otherwise sets it to 0:

  • 3D processing only.
  • Reference: bwmorph3

Smooths 3D objects by reinforcing dominant regions, reducing minor protrusions.

Remove

remove: removes interior voxels (1s surrounded by 1s in 6-connectivity) in the 3D Selection layer, setting them to 0:

  • 3D processing only.
  • Reference: bwmorph3

Hollows out 3D objects, useful for creating shells or isolating boundaries.

Skeleton

skel: removes boundary pixels from the Selection layer without breaking objects, preserving the Euler number to form the image skeleton:

Creates a minimal representation of objects, ideal for analyzing topology or connectivity.

Spur

spur: removes spur pixels (those with one 8-connected neighbor) from the Selection layer, such as line endpoints:

  • 2D processing only.
  • Reference: bwmorph

Cleans up small protrusions or endpoints, refining object shapes.

Thin

thin: thins objects in the Selection layer to lines, shrinking objects without holes to minimally connected strokes and objects with holes to rings halfway between holes and outer boundaries, preserving the Euler number:

Optionally trim small branches with the Remove branches checkbox, useful for simplifying complex structures like networks.

Ultimate Erosion

bwulterode: reduces objects in the Selection layer to points via ultimate erosion:

Produces a minimal set of representative points, ideal for summarizing object locations or centroids.

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