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CellRaft Arrays were used as a culture device for seeding gastrointestinal organoid fragments for studying the effects of microbiota. Using a custom made microinjection system, E. coli was injected into the organoids housed on the CellRaft Array and they were imaged to insure proper injection. The Quad Array allowed for 4 different media chambers to test for different conditions and various antibiotics. The use of this customized hardware modification in conjunction with the CellRaft Array allowed for the development of a semi-automated high-throughput organoid microinjection system that could be reproduced in many laboratories.