Photonic crystal enhanced fluorescence (PCEF) enables a nanostructured dielectric surface to amplify the output of a variety of fluorophore-labeled biomolecule assays for applications that include allergy testing, cancer diagnosis, and viral screening. By increasing fluorescent signals, PCEF enables the achievement of reduced limits of detection with portable and low-cost instrumentation. Expanding the utility of PCEF for disease diagnostics requires the automation, uniformity, and reproducibility of all aspects of the measurement and quantification process, including laser scanning of the PC surface and the subsequent data analysis. In this work, we demonstrate a laser scanning detection instrument, optimal selection of the optical 'on-resonance' incident angle, and automated fluorescence spot intensity analysis that enables PCEF to be utilized for quantification of the concentration of a diagnostic serum antibody (anti-E7) to human papilloma virus infection. The assay is conducted with a single droplet of serum introduced within a PC-integrated microfluidic cartridge that is inserted into the detection instrument.