To resolve the problems of polymerase chain reaction (PCR) chambers iden tification and fluorescence signal extraction in microfluidic real-time PCR system,a data extraction met hod based on algorithm integration is proposed.First,we extract the target region which contains many PCR cham bers from the CCD image. Background and the PCR chambers are separated by the minimum error threshold me thod.The grid method is used to extract a single reaction chamber area.The edge of each reaction chambe r is identified with the wavelet transform and the improved Canny operator.Second,the average gray value of each PCR chamber is calculated and is used as the expression of the gene amplification.A chip with four chambers loading with PUC-18gene is tested by our microfluidic real-time system.The results show that our method c an identify PCR chambers effectively and calculate the intensity of the fluoresc ence signal rapidly.The repeatability of PCR amplification curves is improved by eliminating the influence of the bright and dark spots.The accuracy of gene amplification analysis is also enhanced.