With the steady rise in cases of immune-mediated diseases, extensive studies on environmental, genetic, and epigenetic factors are essential [1]. To facilitate such studies, we developed a platform for advanced allergy profiling, consisting of a microfluidic device with micropillars and an automated processing system. This system is capable of detecting allergy-specific IgEs through the utilization of fluorescence-labelled antibodies. To ensure the platform's accessibility and utility in point-of-care settings and smaller laboratories, we have developed a compact, cost-effective fluorescence reader, enabling the automated readout of the microfluidic chip fluorescence. This novel integration offers promising advancements in the diagnosis and study of allergic conditions, providing a feasible tool in various healthcare and research settings.