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A problem confounding optical imaging technique based on intrinsic signals is the fact that the recorded data contain not only the hemodynamic signal due to the presentation of given sensory stimulation but also several artifacts from respiration, heartbeat, etc. The ultimate goal of analyzing these data sets is to separate the signal that is spatially and temporally specific to a stimulus from more global, non-specific, hemodynamic response(s), and other imaging artifacts. Therefore, pre-processing steps and analysis algorithms are crucial to increase the quality of the data sets. Special software package such as SPM has been designed for the analysis of brain imaging data sequences of fMRI, however, there is no an applicable software package or tools for the analysis of intrinsic optical imaging data sequences. Software based on Matlab has been developed for the analysis of optical imaging based on intrinsic signal data in this paper. Combining with present preprocessing and analyzing methods, the software can effectively isolate the intrinsic signal of optic imaging from the artifacts of different sources, and facilitate researchers analyze intrinsic optical imaging experimental data conveniently.