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The TopoJ plugins help you analyze surfaces of bright objects in image stacks. You can load an example via FileOpen SamplesSinteredAlumina (2.6MB):

Compute Topography

To compute the Topography, call AnalyzeTopoJCompute Topography:

The result looks like this:

Remove Slope

To remove the overall slope of the surface, click on the AnalyzeTopoJRemove Slope menu item: