Modeling nonlinear microscopy near index-mismatched interfaces

Nonlinear microscopy is widely used to characterize thick, optically heterogeneous biological samples. While quantitative image analysis requires accurately describing the contrast mechanisms at play, majority of established numerical models neglect influence field distortion caused by sample heterogeneity near focus. In this work, we show experimentally and numerically that finite-difference time-domain (FDTD) methods are applicable model focused fields interactions in presence heterogeneities, typical nonlinear microscopy. We analyze ubiquitous geometry a vertical interface between index-mismatched media (water, glass, lipids) consider cases two-photon-excited fluorescence (2PEF), third-harmonic generation (THG) polarized THG contrasts. FDTD simulations can reproduce experimental images obtained on samples live adult zebrafish, with previous neglecting distortions index mismatch micrometer scale. Accounting for these effects appears be particularly critical when interpreting coherent polarization-resolved data.