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Morphological 2D/3D Operations

Overview

Morphological Ops

Applies morphological operations to the Selection layer using MATLAB's bwmorph, bwmorph3, bwskel, and bwulterode functions.

The available operations depend on the 3D objects checkbox — switching it repopulates the Morphological operation dropdown with the operations relevant to the chosen dimensionality.

Demonstration
Skeleton for 3D objects

Controls

  • Morphological operation: the operation to apply (see 2D operations and 3D operations below).

  • : when checked, uses 3D operations (bwmorph3 / bwskel); when unchecked, uses 2D operations (bwmorph). Switching repopulates Morphological operation.

  • Apply to (2D mode only):

    • Current slice — applies the operation to the currently displayed slice.
    • Stack — applies to every slice in the Z-stack.

  • Iterations:

    • Limit to N / Infinite: choose a fixed iteration count or run until convergence. For Skeleton, only Limit to is available and the value is used as Min branch length. For 3D operations other than Skeleton, iterations are not applicable and these controls are disabled.
    • Iterations number / Min branch length: the spinner value (label changes based on the selected operation).

  • : removes small branches after thinning or skeletonisation. Available for Skeleton (2D) and Thin with Infinite iterations (2D).

  • Ultimate erosion panel (visible only when bwulterode is selected in 2D mode):

    • 2D / 3D: selects the connectivity dimension for the erosion.
    • Connectivity: 4 or 8 in 2D mode; 6, 18, or 26 in 3D mode.
    • Method: distance metric — euclidean, cityblock, chessboard, or quasi-euclidean.

  • (2D mode only): updates the preview automatically on every widget change.

  • Preview (2D mode only): overlays the result on the current view without committing changes.
  • Apply: applies the operation to the Selection layer.
  • Close: closes the dialog without making changes.

2D operations

Available when is unchecked.

Branch points

branchpoints — finds branch points (junctions) of a skeleton:

  • Pixels where multiple skeleton branches meet are set to 1; all others to 0.
  • The image must be skeletonised first.
  • Reference: bwmorph

Diagonal fill

diag — eliminates 8-connectivity of the background using diagonal fill:

  • Fills diagonal gaps so that background regions lose 8-connectivity: 1 0 → 1 1 / 0 1 → 1 1
  • Reference: bwmorph

Endpoints

endpoints — finds end points of a skeleton:

  • Pixels with only one 8-connected neighbour are set to 1.
  • Reference: bwmorph

Skeleton

skel — reduces objects to 1-pixel-wide skeletons using bwskel:

  • Removes boundary pixels without breaking connectivity; preserves the Euler number.
  • The Limit to value is used as Min branch length (branches shorter than this are pruned).
  • applies additional branch removal after skeletonisation.
  • Reference: bwskel
    Demo

Spur

spur — removes spur pixels (pixels with exactly one 8-connected neighbour):

  • Cleans up isolated line endpoints produced by skeletonisation or thinning.
  • Reference: bwmorph

Thin

thin — thins objects to lines:

  • Objects without holes shrink to minimally connected strokes; objects with holes shrink to rings.
  • Preserves the Euler number.
  • With Infinite iterations and checked, small branches are removed from the result.
  • Reference: bwmorph
    Demo

Ultimate erosion

bwulterode — reduces objects to their ultimate eroded points (local maxima of the distance transform):

  • Each connected object is reduced to one or more isolated representative pixels.
  • Configure the erosion via the Ultimate erosion panel:
    • Mode (2D / 3D) and Connectivity control how neighbourhoods are defined.
    • Method selects the distance metric (euclidean, cityblock, chessboard, quasi-euclidean).
  • Reference: bwulterode

3D operations

Available when is checked. All operations process the full 3D stack; Apply to is fixed to Stack. Iterations are not applicable except for Skeleton.

Branch points

branchpoints — finds branch points of a 3D skeleton:

  • Voxels at skeleton junctions are set to 1; all others to 0.
  • The volume must be skeletonised first.
  • Reference: bwmorph3

Clean

clean — removes isolated voxels:

  • An isolated voxel is a single voxel set to 1 completely surrounded by voxels set to 0.
  • Reference: bwmorph3

Endpoints

endpoints — finds end points of a 3D skeleton:

  • Voxels with only one 26-connected neighbour are set to 1.
  • Reference: bwmorph3

Fill

fill — fills isolated interior voxels:

  • Isolated interior voxels (set to 0 and surrounded 6-connected by voxels set to 1) are set to 1.
  • Reference: bwmorph3

Majority

majority — keeps a voxel set to 1 only if the majority of its neighbourhood is 1:

  • A voxel stays 1 if ≥ 14 of the 26 voxels in its 3×3×3 neighbourhood are 1; otherwise set to 0.
  • Reference: bwmorph3

Remove

remove — removes interior voxels:

  • Interior voxels (set to 1 and surrounded 6-connected by voxels set to 1) are set to 0, leaving only the object surface.
  • Reference: bwmorph3

Skeleton

skel — reduces 3D objects to 1-voxel-wide skeletons using bwskel:

  • The Limit to value is used as Min branch length; branches shorter than this are pruned.
  • Reference: bwskel
    Demo

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