The Eternal Cylinder

Mineral ingredients, like rocks or gems, are denoted in your inventory with a crystal logo in the upper right of the icon, and cannot generally be eaten. They are mostly found in caves.

In order to process minerals, you need a Trebhum with the mineral processor mutation. You can obtain it by eating a Lithotroph Mushroom, which looks like a circular crown made of fungus and is generally found resting on statues inside caves and shrines.

Once a Trebhum has the mutation (which will make it look like it has multiple exhaust pipes around its head), any mineral ingredient in its inventory will automatically begin processing over time. Just give them to the Trebhum and wait. Mineral are processed into crystal which is spent to upgrade and revive dead Trebhum.

Throughout the game you’ll have many chances to find a mushroom like ring in caves or on trebum statues. Have one of your party members eat it and they will be able to process any mineral you come across.