DNA microarrays technology is a powerful method to monitor the activity of thousands of genes simultaneously in a cell. An impressive amount of data is being collected in "wet labs" all over the world. A large microarray instrument can easily analyze and record in a day the expression profiles of say, tens of thousands of genes. The output is typically in the tens of MBytes, and can be easily reach in the hundreds of MBytes of raw data. It is believed crucial to keep the raw data in some permanent storage medium. Repeating the experiment is usually not viable because of the high costs associated with this new technology. Some form of data compression is therefore required.

Here, we propose a simple and effective lossless compression system for microarray images. The system can automatically locate both grids and individual spots and compress the microarray image without any other input parameters and human intervention. Based on our preliminary tests, the tool is quite robust to images with variable quality.

Automatic Grid and Spot Finding in Microarray Images

We try to develop a tool that can find the grids and spots in a microarray images totally automatically, without any human interactions. This tool can find and decide the numbers of rows and columns of sub-grids and also finding each spot showed in the images.

Results Demo:

Download the Grid image here (1.7Mb/8bits/gif)

Download the Spot image here (1.7Mb/8bits/gif)

Lossless Compression of Microarray Images

With the recent explosion of interest in microarray technology, massive amounts of microarray images are currently being produced. The storage and the transmission of this type of data are becoming increasingly challenging. Here we propose lossless and lossy compression algorithms for microarray images originally digitized at 16 bpp that achieve an average of 9.5-11.5 bpp (lossless) and 4.6-6.7 bpp (lossy, with a PSNR of 63dB). The lossy compression is applied only on the background of the image, thereby preserving the regions of interest. The methods are based on a completely automatic gridding procedure of the image.

Our test microarray images:

Array1 (7Mb/16bits/tif)

Array2 (20Mb/16bits/tif)

Array3 (13Mb/16bits/tif)

Publication

S.Lonardi, Y.Luo, "Gridding and Compression of Microarray Images"

IEEE Computational Systems Bioinformatics Conference (CSB'04)

Stanford, CA, August 2004.

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Last Update: 8/13/2004