Selection Menu

Actions that can be applied to theSelectionlayer. TheSelectionis one of three main segmentation layers (Model, Selection, Mask) which can be used in combibation with other layer. See more about segmentation layers inthe Data layers of Microscopy Image Browser section.

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Contents

Selection to Buffer

Allows to Copy (Ctrl+Cshortcut) theSelectionof the currently shown slice to a buffer, which later can be pasted to any other slice with theCtrl+Vshortcut 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).

..->Mask

Allows the modification of theMasklayer by the contents of theSelectionlayer. 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:
https://youtu.be/L-w8eGDfUkU
Skeleton for 3D objects, https://youtu.be/Au4vb7max9Q

Performs morphological operations for 2D and 3D objects of theSelectionlayer. See more in the description of MATLABbwmorph,bwmorph3andbwskelfunctions. The following operations are available:

• Branch points- (2 d / 3 d)找到分支点的骨架;
• Clean- (3D) remove isolated voxels;
• Diagonal fill- (Diag) uses diagonal fill to eliminate 8-connectivity of thebackground;
• End points- (2D/3D)finds end points of skeleton;
• Fill- (3D) Fill isolated interior voxels, setting them to 1.
  Isolated interior voxels are individual voxels that are set to 0 that are surrounded (6-connected) by voxels set to 1;
• Majority- (3D) Keep a voxel set to 1 if 14 or more voxels (the majority) in its 3-by-3-by-3, 26-connected neighborhood are set to 1; otherwise, set the voxel to 0;
• Remove- (3D) Remove interior voxels, setting it to 0.\nInterior voxels are individual voxels that are set to 1 that are surrounded (6-connected) by voxels set to 1;
• Skeleton- (Skel, 2D/3D) with n = Inf, removes pixels on the boundaries of objects but does not allow objects to break apart. The remaining pixels make up the image skeleton. This option preserves the Euler number;
• Spur- removes spur pixels, i.e. the pixels that have exactly one 8-connected neighbor. For example, spur essentially removes the endpoints of lines
• Thin- with n = Inf, thins objects to lines. It removes pixels so that an object without holes shrinks to a minimally connected stroke, and an object with holes shrinks to a connected ring halfway between each hole and the outer boundary; this option preserves the Euler number. Use the "remove branches" option to remove small branches from each line profile
• Ultimate erosion, (2D/3D) performs ultimate erosion, i.e. object -> to point

Expand to mask borders

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

Interpolate

Interpolation of theSelectionlayer is a method to reconstructSelectionon empty slices between two slices containing theSelectionlayer. Shortcut for this action isi.

There are two types of interpolators. Select the best suitable interpolator in thePreferences dialogor by pressing the Interpolator type button in theToolbar:

A brief demonstration is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=4m3s

A brief demonstration is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=2m22s

Please note!there should be only one object in theSelectionlayer 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:
https://youtu.be/fNz1vGq7Hb0

Smooth selection

Smoothes theSelectionlayer in 2D or 3D space.

Invert selection

Inverts the current selection for the whole dataset.

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Published with MATLAB® R2021b