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'Amygdules' form when the vesicular cavities (created by expanding gas bubbles in volcanic lava) are filled with a secondary mineral such as calcite, quartz, chlorite or one of the zeolites, which are deposited by having minerals "wash" through the pores in the rock (see Porosity/Permeability). They are filled from the outside, making some amygdules concentrically layered.
"Amygdules" refer to the smaller ones.
"Amygdales" refer to the larger ones and is more common in British usage.