In this paper, we present a method of recognizing the barcodes of individual strips using a single camera in a quantitative fluorescence analysis system that can process multiple lateral-flow strips simultaneously. The proposed method eliminates the need for multiple scanners or a scanning mechanism. The presence or absence of strips in each slot was determined, and the position of the start bit was detected by template matching to find the barcode area. After the start bit was located, the rest of the bit area was found using the barcode dimensions and the estimated image spatial resolution obtained while calibrating the instrument. The value of each bit was determined using the average along the central line with 60% of the width of the bit area. Sixteen cartridge images were obtained under various illuminations to statistically evaluate the thresholds for the investigation of various parameters, such as the existence of the strip, the successful detection of the start bit position, and each bit value. The threshold values were determined using the two-class mixed Gaussian model to minimize errors. Experimental results show that the error rates for all parameters were negligible.