Automated analysis of label-free spinning-disc microarray images

Abstract

We describe a set of methods to enable fully automated analysis of a novel label-free spinning-disc format microarray system. This microarray system operates in a dual-channel mode, simultaneously acquiring fluorescence as well as interferometric signals. The label-free interferometric component enables the design of robust gridding methods, which account for rotational effects difficult to estimate in traditional microarray image analysis. Printing of microarray features in a Cartesian grid is preferable for commercial systems because of the benefits of using existing DNA/protein printing technologies. The spinning disc operation of the microarray requires spatial transformation of Cartesian microarray features, from the reader/scanner frame of reference to the disc frame of reference. We describe a fast spatial transformation method with no measurable degradation in the quality of transformed data, for this purpose. The gridding method uses frequency-domain information to calculate grid spacing and grid rotation. An adaptive morphological segmentation method is used to segment microarray spots with variable sizes accurately. The entire process, from the generation of the raw data to the extraction of biologically relevant information, can be performed without any manual intervention, allowing for the deployment of high-throughput systems. These image analysis methods have enabled this microarray system to achieve superior sensitivity limits.