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This paper reports the design of an innovative CMOS active pixel sensor (CAPS) using Silicon-on-Insulator (SOI) technology. The CAPS designs approach provides the flexibility and high density features of hybrid pixel sensors with photon integration architecture. This sensor is the key component for the optimized biomarker scanner. A proof-of-principle test chip, paying particular attention to the noise performance of the pixel, the conversion gain, front-end electronics (FEE) and readout speed, can be available for testing in 2009. The overall objective of this paper is to contribute to improved diagnosis, prognosis, and prediction of breast cancer disease through the development of a very high conversion gain, low noise Photon Integration CMOS Imager. The design target for fluorescent detection limit with the CAPS is 4.49 fluorophores / mum2.