Separating crystalline material from the mother liquor is often performed by filtration, whereas different options to generate the driving force are possible to use. However, the separation process can affect the structure of crystalline material, either by breakage events or agglomeration. In this work, a method of automated image analysis was used to evaluate the agglomeration degree of two crystalline amino acids after a pressure or vacuum filtration. The information resulting from this consideration enables to adjust the crystal structure depending on the individual filtration type.