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In this study, new magnetic manganese ferrite (MnFe2O4) nanoparticles with a size around 100 nanometer (nm) in diameter were used to improve the performance of an immunoassay for detection of influenza infection. A new microfluidic system was developed to automatically implement the entire detection process. In order to apply these new nanoparticles for influenza detection, the design of the micromixer was optimized to reduce the dead volume. Furthermore, a custom-made control system was used for automating the entire chip operation. The synthesized nanoparticles were tested for three months to confirm the stability of the process of thermal decomposition. Furthermore, with the custom-made control system, mixing index of the modified micromixer can be as high as 96% in 2 seconds under both positive and negative air forces under a driving frequency of 4Hz. The optical signals showed that this nanoparticle-based immunoassay could successfully achieve a limit of detection as low as 0.03 Hau. This developed microfluidic system can automatically perform the entire process involved in the immunoassay, including virus purification and detection, and therefore may provide a promising platform for fast diagnosis of the infectious diseases.