Apply Mask

Input

Either: 1. Any 2D or 3D image or image set, to apply the mask on 2. A 2D or 3D image (not image set) with the same dimensions as all images in input 1, defining the mask

Or: 1. A single 2D or 3D image that has a mask attached (see “Edit Mask” in the context menu of the image)

Output

A copy of the masked image or image set, if the Create new image flag is enabled

Description

The mask provided in the second input is applied to the first input. The intensities of the input image are set to zero outside of the mask. A pixel is defined as inside the mask if the mask intensity value is above the Threshold value for the flag Threshold above set to true, and outside otherwise. If Crop automatically is enabled, the output image will be cropped to the bounding box of the masked voxels.