Cropping 3D label image results in shifted label object wrt intensity image #50
Description
Obviously, cropping in 3D (using the shapes layer) also affects the transparent part of the label image (label id 0), thus changing label image shape. This is undesired if the label image is required for downstream analysis including the original/intensity image. It is not explicitly mentioned in the plugin description that cropping also affects label id 0. -> Feature request: It would be favorable to be able to select the label id(s) that are cropped.