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Fluorescence diffuse optical tomography(FDOT)is an emerging cost-effective modality for small animal imaging.It allows one to obtain quantitative functional measurements,and enables the threedimensional localization of fluorescent targeted region.Compared to other functional imaging modalities such as positron emission tomography,FDOT is cheaper and easier to use.The continuous-wave system allows noncontact measurements and does not require the immersion of animal in an optical adaptation liquid.After being injected with a cancer specific marker,the animal is scanned with near-infrared light over the brain.The system records the outgoing transmitted and emitted fluorescence light,and then the 3-D fluorescence image is reconstructed to infer cancer localization and activity.To carry out in vivo experiments on small animals,the heterogeneous optical properties and complex shaped object geometries must be taken into accountin the reconstruction method.Therefore,a new reconstruction method is proposed for this purpose.Furthermore,FDOT can provide important information in biomedical studies.In some ill-posed problems,suppression of autofluorescence of background tissue is of utmost importance.Therefore,we develop a new system and its associated reconstruction method.It is able to reconstruct the fluorescence yield even in heterogeneous and highly attenuating body regions such as brain.Some phantom experiments validate the performance of this new system for heterogeneous media inspection.A method is proposed for autofluorescence-insensitive FDOT,which employs nanoparticles in a tissue phantom under excitation intensities well below tissue-damage thresholds.Reconstruction artifacts that commonly plague Stokes-shifting fluorophores can be effectively suppressed.The main advantage of the FDOT system is its ability to reconstruct the fluorescence yield even in heterogeneous and highly attenuating body regions such as glioma.