On the Bitplane Compression of Microarray Images

The microarray image technology is a new and powerful tool for studying the expression of thousands of genes simultaneously. Methods for image processing and statistical analysis are still under development, and results on microarray data from different sources are therefore rarely comparable. The urgent need for data formats and standards is recognized by researchers in the field. To facilitate the development of such standards, methods for efficient data sharing and transmission are necessary, that is compression. Microarray images come in pairs: two high precision 16 bits per pixel intensity scans (“red” and “green”). The genetic information is extracted from the two scans via segmentation, background correction and normalization of red-to-green image intensities. We present a compression scheme for microarray images that is based on an extension of the JPEG2000 lossless standard, used in conjunction with a robust L1 vector quantizer. The L1 vector quantizer is trained on microarray image data from a replicate experiment. Thus, the image pairs are encoded jointly. This ensures that the genetic information extraction is only marginally affected by the compression at compression ratios 8:1.