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Morphology-transport relationships are a key feature of chromatographic separation processes, which are still under investigation.In order to quantify the correlation between morphology and separation processes (e.g., effective diffusion, axial dispersion) a three-dimensional reconstruction of the stationary phases is desirable.This is possible for silica-based monoliths using confocal laser scanning microscopy (CLSM) [1,2].We describe the method of achieving a three-dimensional reconstruction and how to evaluate the reconstructed structure in view of the characterization of the pore-size and porosity distributions as well as quantifiable parameters for structural heterogeneity.