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This work is motivated by the need for accurate positioning of both adherent and non-adherent cells into arrays that can be integrated with microfluidic channels in high-throughput screening (HTS) for drug discovery. We describe a microfluidic device that allows rapid production of uniform micro hydrogel capsules that can contain cells. Up to 1times104 hydrogel capsules can be simply formed and arrayed simultaneously using microchambers in a 10 mm long microchannel. In this work, alginate was used as the hydrogel capsules that can be dissolved and removed with EDTA; thus samples confined in the capsules are collectable after observation in the array. We demonstrated the microencapsulation of E. coli into alginate capsules, and dissolved the capsules with EDTA successfully.