Mask Menu

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 combibation with other layer. See more about segmentation layers in the Data layers of Microscopy Image Browser section.

Back to Index --> User Guide --> Menu



Allows modification of the Selection layer by the Mask layer. It is possible to replace the selection with the mask, add mask to the selection, or remove mask from the selection. These actions can be applied for the currently shown slice or for the whole volume.

Clear mask

Clears the mask, i.e. deletes the Mask layer from the memory.

Load mask

Load mask from disk. The mask is saved in the Matlab format with the *.mask extension.

Import Mask from Matlab

Imports mask from the main Matlab workspace. The mask should be a matrix with dimensions similar to those of the loaded dataset [1:height, 1:width, 1:no-slices] of the uint8 class.

Export Mask to Matlab

Exports mask to the main Matlab workspace, the exported mask may be imported back to im_browser using Import Mask from Matlab command.

Save mask as...

Saves mask to disk. The mask is saved in the Matlab format with *.mask extension.

Invert mask

Inverts mask so that the masked areas become background and the background becomes a mask.

Size exclusion filter

Filters the mask based on size of the objects within this mask. It is possible to filter 2D or 3D objects. The minimal and the maximal sizes of the objects are asked in the first two edit boxes of the corresponding dialog. Note! It might be handier to use the Mask Statistics... option.

Replace masked area in the image.

Replaces image intensity in the masked areas with new values. A new dialog would ask to provide new intensities, slices, and the color channels.

A brief demonstration is available in the following video:

Smooth mask

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

Mask Statistics

Get statistics for the mask layer. See more here

Back to Index --> User Guide --> Menu