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Flow cytometry is an electrical detection system that provides precise and diverse optical properties to cells and micro particles. Flow cytometry, which provides multidimensional information including cell size and granularity through light scattering and fluorescence emission generated by the induction of light of a specific wavelength to the fluorescently treated cells or micro particles, plays an important role in biomedical and biophysical fields. However, it has some drawbacks such as high cost, size of the instrument and limitation in selecting fluorescent dyes. Therefore, in this paper, a low cost compact fluorescent detection system is developed using light-emitting diode and microcontroller. The proposed fluorescence detection system has a replaceable the light source/fluorescence filter/photodetector and constructed by 3D printer, so that the user can design a customized system according to the selected fluorescent dyes. The fluorescence intensity was measured by varying the number of fluorescently labeled cells, and the measured intensities showed a high linearity within the tested concentration ranges. [ABSTRACT FROM AUTHOR]