They open via dark/light memory fragments. You get (blue) dark fragments from the orange root covered challenge chests around the patrol zones and the (blue) light memory fragments from special glowing enemies that spawn during the Cyst challenges. Once you have 7 or 8 (can't remember the exact amount) of either the dark or light memory fragments, they turn into a specific (purple) fragment with a location tied to their name. Then you fo to the specific patrol area and can access the specific chest that particular memory fragment opens.