Mask Generators panel

This panel hosts several ways of automatic mask generation. Specific areas of interest from the generated mask may further be selected for segmentation. See more about masks.

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Common fields

There are several common fields that do not depend on type of the selected mask generator.

the whole dataset in the 2D mode, i.e. slice by slice; 3D use the 3D mode for the mask generation

3. Do it button:

Frangi Filter

Hessian based Frangi Vesselness filter, written by Marc Schrijver and Dirk-Jan Kroon. This function uses the eigenvectors of the Hessian to compute the likeliness of an image region to contain vessels or other image ridges, according to the method described by Frangi 1998, 2001.

Note, to work properly this function should be compiled. See details in System Requirements


Morphological filters

Set of Matlab based morphological filters.

Strel Filter

Generate mask based on morphological image opening and black-and-white thresholding. The function first performs morphological bottom-hat (Black on white is checked) or top-hat (Black on white is unchecked) filtering of the image. The top-hat filtering computes the morphological opening of the image (using imopen) and then subtracts the result from the original image. The result is then black and white thresholded with parameter in the B/W threshold edit box.

  1. Strel size, defines size of the structural element (disk type) for imtophat and imbothat filtering.
  2. Fill checkbox, check it to fill holes in the resulted Mask image.
  3. B/W threshold, specifies parameter for the black and white thresholding.
  4. Size limit, limits the size of generated 2D objects so that objects smaller than this value are removed from the Mask during the filter run.
  5. Black on white checkbox, when checked, the filter will use morphological bottom-hat filtering (imbothat). When unchecked - morphological top-hat filtering (imtophat).

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