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Handling of microorganisms is of great interest in biology and biotechnology. Single cell capture technology has been demonstrated in our previous work with thermal gelation material and micro fluidic devise. This paper extends the system by local flow rate control to stabilize the trap with in-situ fabrication by photo-crosslinkable resin. Target cells are captured by gel and enclosed with the micro-structure. The cells, therefore, are protected from high-speed-channel flow or disturbances. This system succeeds in the separation and continuous culture of yeast cells, reaction and monitoring of the cultured cells stably by fluorescence staining in situ on a chip.