Scanning of arrays after hybridization or binding assays is done with ScanArray Express Microarray Scanner, which uses high quality gas lasers for green, red and orange fluorescent dyes. The system is software driven for image acquisition and quantitative analyses. It uses gal file generated by our printer to incorporate data on gene location and identification in the output result files. The software supports four output image file formats, TIFF, BMP, JPEG, and Raw. Informatics ready results are output in CSV and GPR formats for easy data integration and conversion into Excel format. We can provide to our clients output image and quantitative data files on CDs. Further detailed analysis will be done separately if requested.

Scanning is done by con-focal technology that allows for higher signal-to-noise ratios. The dual wavelength arrays are scanned sequentially with provision to continuously adjust laser power and PMT gain. This is useful to achieve maximum dynamic range and hence the greatest sensitivity. The final image resolution can be adjusted to 10, 20, 30 and 50 microns to match the right resolution required for the feature size to be scanned. As the arrays are scanned, images are generated for query and control samples typically as 16-bit TIFF images and can be quantified employing different quantitation methods.

The quantitation process involves identification of spots with real signals from other artifacts. We recommend use of Gal file generated for each particular type of array, which includes gene list and information on the location of each spot on the array. This allows alignment of spots in the displayed images with their corresponding grid template. Some finer adjustments of the grid are done manually within the arrays and sub-arrays. Once the spots are identified, the next step is to define areas within each cell of the grid that contribute to spot signal and background. This is achieved by selecting different quantitative methods, which allow different statistical options. The most preferred of these methods are Fixed Circle and Adaptive Circle. Further, data should be normalized for measured hybridization intensities in the 2 channels in order to accurately determine differences in gene expression. All these features are included in the QuantArray software provided with the scanner.By selecting any of these options, raw data is generated that includes measures such as Total, Median and Mean of spot signal and background intensities as well as other statistics such as standard deviation of both signal and background etc. Different approaches can be adopted to measure fluorescence intensities of spots on the arrays based on customer requirements.