Microarray technology is a new and powerful tool for concurrent monitoring of large number of genes expressions. Each microarray experiment produces hundreds of images. Each digital image requires a large storage space. Hence, real-time processing of these images and transmission of them necessitates efficient and custom-made lossless compression schemes. In this paper, we offer a new architecture for lossless compression of microarray images. In this architecture, we have used a dedicated HARDWARE for separation of foreground pixels from the background ones. By separating these pixels and using pipeline architecture, a higher lossless compression ratio has been achieved as compared to other existing methods.