Hey, as a part of our Masters' project, we are trying to register a stack of histological slices and then we can easily see them with "Image->Stacks->Orthogonal views" or "Plugins->Volume viewer" for example. But what we also would like to do is reconstruct a 3D surface viewable in "Plugins->3D viewer". After registration, many of the slices have black background because of registering. How do we go about this problem to make only the blue parts stand out in the image and ALL the rest leave BLACK? Or in other words, leave out the background so that we get a 3D model? Any help will be highly appreciated, thanks!