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A cortex chip is a type of computer chip designed to store A.I. It has a universal connector, allowing it to be inserted into machinery, such as robots or Omnitools. It may also contain a person's brain scan and will create a Mockingbird if inserted into a device. When paired with Structure Gel, the Cortex Chip can be used to animate a facsimile of a human body.
They seem to come with in-built audio recording and processing software in order to process sounds and voices and interact accordingly; there is also a version of the Cortex Chip with an inbuilt camera, which provides the scanned person with visual capabilities. Cortex Chips are not designed to handle complex AIs and so if loaded with a brain scan they may overload and explode if the AI experiences extreme emotions.
Simon Jarrett obtains two Cortex Chips over the course of the game. One contains a brain scan of Catherine Chun, which he connects to his Omnitool. He uses the other to build a second body for himself to be able to survive the extreme water pressure of the abyss.