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Mask Menu

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Overview

Actions that can be applied to the Mask layer. The Mask layer is one of three main segmentation layers (Model, Selection, Mask) which can be used in combination with other layers. See more about segmentation layers in the Data layers section.

Mask Menu

..→Selection

Mask to selection

Allows modification of the Selection layer using the Mask layer.

Options include

  • replacing the Selection with the Mask
  • adding the Mask to the Selection
  • removing the Mask from the Selection.

Info

These actions can apply to the currently shown slice or the entire volume.

Clear mask

Clears the Mask layer, deleting it from computer memory.

Load mask

Loads a mask from disk. By default, masks are saved in MATLAB format with the *.mask extension.

It is possible to load masks from variety of image formats:

  • .mask - MATLAB format
  • .am - Amira Mesh labels
  • .h5 - Hierarchical Data Format (hdf5)
  • .tif - TIF format
  • .xml - Hierarchical Data Format with XML header (hdf5)
  • All files - it should be possible to load standard image formats as masks

Masks

Masks can only contain a single material

Import Mask from

Imports a mask from the main MATLAB workspace or another dataset opened in MIB.
The mask must be a matrix matching the dataset dimensions [1:height, 1:width, 1:no-slices] of uint8 class.

Export Mask to

Exports the mask to the main MATLAB workspace or another dataset opened in MIB.
The exported mask can be re-imported using Import Mask from MATLAB.

Save mask as...

Saves the mask to disk.
By default, it uses MATLAB format with a *.mask extension and Mask_ prefix.

List of available formats to save masks
  • MATLAB format (.mask): Default format for saving masks.
  • Amira mesh binary (.am): Amira Mesh binary format.
  • Amira mesh binary RLE compression SLOW (.am): Compressed Amira Mesh format.
    !!! warning Not recommended due to slow performance. Use Amira mesh binary and resave with RLE compression in Amira instead.
  • Hierarchical Data Format (.h5): Chunked format suitable for Ilastik.
  • PNG format (.png): Saves mask as 2D slices in Portable Network Graphic format.
  • TIF format (.tif): Saves mask as 2D slices or 3D volumes in Tag Image File format.
  • Hierarchical Data Format with XML header (.xml): Generates an HDF5 file and an XML file with image parameters.

Invert mask

Inverts the mask, turning masked areas into background and background into a mask.

Replace masked area in the image

Replace Color

Replaces image intensity in masked areas with new values.
A dialog prompts for new intensities, slices, and color channels.

Demonstration

Smooth mask

Replace Color

Smooths the Mask layer in 2D or 3D space.

Mask smoothing

It is recommended to use Image Filters for interactive evaluation of smoothing results

Mask Statistics

Gets statistics for the mask layer material, usable to filter the mask by object properties.

Start quantification directly from the Segmentation table

Accessible also via
Segmentation Panel → Materials List → Right-click → Get statistics...
See Mask and Model Statistics for details.

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