Fast Spot Locating for Low-density DNA Microarray

Low-density DNA microarrays are pivotal in molecular diagnostics due to their cost-effectiveness, high sensitivity, and ease of use. However, reliable spot localization remains a challenge, primarily due to variations in spot positions resulting from printing and alignment inaccuracies, as well as the presence of image artifacts. Traditional intensity-based methods are often inadequate, particularly when target spots exhibit weak fluorescence signals. In this study, we propose a rapid spot localization method that combines spot template matching with point pattern matching, enhanced through vectorized programming and the use of square (box) templates. By replacing circular templates with box templates, separable filtering and moving average techniques can be applied, significantly reducing computational overhead without compromising detection performance. The proposed method not only overcomes the intensive computation associated with normalized cross-correlation but also improves overall efficiency, making it highly suitable for high-throughput and resource-constrained diagnostic applications. Validation was performed using images obtained from HPV genotyping of actual patient samples on a commercial DNA microarray, confirming the method’s practical applicability in a clinical setting.