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Mask Generators Panel

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Overview

The Mask Generators Panel offers automated methods to create masks based on specific criteria or algorithms. These masks are useful for segmentation or targeting areas of interest. Learn more in Data Layers.

Common fields

Common Fields

These controls apply across all mask generators:

  • 1. Filter type: select a mask generator from the list.
  • 2. Mode radio buttons:
    • Current: generates a mask for the current slice only.
    • 2D all: generates masks for all slices using a 2D approach.
    • 3D: generates a mask for the entire dataset in 3D.
  • 3. Do it button:
    • : Starts the selected generator, replacing the existing mask.
    • → Do new mask: Starts the generator, replacing the existing mask.
      Dropdown Menu
    • → Generate new mask and add it to the existing mask: Adds the new mask to the existing one.
      Useful for multidimensional filtering:
      1. Run generator for XY.
      2. Switch to XZ or YZ via the Toolbar.
      3. Run generator again with this option.

Frangi Filter

Frangi Filter

Based on Marc Schrijver and Dirk-Jan Kroon’s Hessian-based Frangi Vesselness filter, this uses Hessian eigenvectors to detect vessels or ridges (Frangi 1998, 2001).

May require compilation; see System Requirements.

Parameters
  • Range: Sigma range (default: [1-6]).
  • Ratio: Step size between sigmas (default: 2).
  • beta1: Frangi correction constant (default: 0.9).
  • beta2: Frangi correction constant (default: 15).
  • beta3: Vesselness threshold (default: 500; rule of thumb: vessel greyvalues ÷ 4–6).
  • B/W threshold: Threshold for Mask layer; 0 yields a filtered image instead of binary.
  • Object size limit: Removes 2D objects smaller than this value post-filtering.
  • Black on white: Detects black ridges on white background when checked.

Morphological Filters

Morphological Filters

MATLAB-based morphological filters

Extended-Maxima Extended-maxima transform: Uses MATLAB’s imextendedmax to find regional maxima in the H-maxima transform (constant-intensity regions with lower external boundaries).

Extended-Minima Extended-minima transform: Uses imextendedmin for regional minima in the H-minima transform (constant-intensity regions with higher external boundaries).

H-Maxima H-maxima transform: Suppresses maxima below an H-value, then thresholds with a specified value. Regional maxima have constant intensity and lower external boundaries.

H-minima transform: Suppresses minima below an H-value, then thresholds. Regional minima have constant intensity and higher external boundaries.
Regional maxima: Uses imregionalmax to create a binary mask of regional maxima (1 for maxima, 0 otherwise).
Regional minima: Uses imregionalmin for a binary mask of regional minima (1 for minima, 0 otherwise).

Strel Filter

Strel Filter

Generates a mask via morphological opening and black-and-white thresholding.
Uses bottom-hat filtering (imbothat ) if Black on white is checked, or top-hat (imtophat ) if unchecked, followed by thresholding.

  • Strel size: Sets the disk-type structural element size for imtophat/imbothat.
  • Fill: Fills holes in the resulting Mask.
  • B/W threshold: Sets the black-and-white thresholding parameter.
  • Size limit: Removes 2D objects smaller than this value from the Mask.
  • Black on white: Uses bottom-hat filtering when checked, top-hat when unchecked.

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