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IMBED is an ingestible diagnostic capable of in vivo biosensing in harsh, difficult-to-access environments such as the stomach. The system encapsulates biosensor bacteria adjacent to the readout electronics in individual wells separated from the outside environment by a semi-permeable membrane that confines sample cells within the device. The biosensor bacteria utilizes bioluminescence to generate light when sensing target biomarkers within the sample cells. Photodetectors sense the light, and a wireless transmitter sends the biomarker information to an external device for convenient readout.