A method of monitoring a time-varying fluorescence emitted from a fluorescent agent from within a diffuse reflecting medium with time-varying optical properties is disclosed that includes providing at least two measurements obtained from a patient before and after administration of the fluorescent agent that includes an Flrmeas signal detected adjacent to the medium by a filtered light detector during illumination of the medium by excitatory-wavelength light, and at least one DR signal selected from: a DRexmeas DRem, and DRem,filtered signal. The method further includes identifying a post-equilibration portion of the measurement data set and transforming each Flrmeas signal within the post-equilibration portion of the measurement data set to an IFagent signal representing a detected fluorescence intensity emitted solely by the fluorescent agent from within the medium. The disclosed method includes removing the effects of leak-through of excitation-level light and removing the effects of autofluorescence from the Flrmeas signal.