Selection Menu

Actions that can be applied to the Selection layer. The Selection 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.

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Selection to Buffer

Allows to Copy (Ctrl+C shortcut) the Selection of the currently shown slice to a buffer, which later can be pasted to any other slice with the Ctrl+V shortcut or to all slices (Ctrl+Shift+V). In addition there is an option to clear the buffer (Menu->Selection->Selection to Buffer->Clear); this action clears only the buffer and does not affect any of the other layers (Selection, Mask, Model).


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

Morphological 2D/3D operations

A brief demonstration is available in the following videos:
Skeleton for 3D objects,

Performs morphological operations for 2D and 3D objects of the Selection layer. See more in the description of Matlab bwmorph, bwmorph3 and bwskel functions. The following operations are available:

Expand to mask borders

Each selected area will be expanded to match the borders of the mask that contains selected area.


Interpolation of the Selection layer is a method to reconstruct Selection on empty slices between two slices containing the Selection layer. Shortcut for this action is i.

There are two types of interpolators. Select the best suitable interpolator in the Preferences dialog or by pressing the Interpolator type button in the Toolbar:

A brief demonstration is available in the following video:

A brief demonstration is available in the following video:

Please note! there should be only one object in the Selection layer on the starting and ending slices.

Replace selected area in the image

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

A brief demonstration is available in the following video:

Smooth selection

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

Invert selection

Inverts the current selection for the whole dataset.

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