When using infrared lasers (800-1300nm), scattering and absorption loss can be greatly reduce for in vivo microscopy, thus achiving deep tissue observation. To improve spatial resolution and imaging contrast, femtosecond lasers with ~100fs pulse width are employed as excitation light sources. Tagged fluorophores can be two-photon excited, thus achieving intrinsic sectioning images. Besides, second harmonic generation (SHG) contrast can reveal structure proteins like collagen, muscles, myelin sheath, and spindle fibers without a labeling . Third harmonic generation (THG) contrast is sensitive to inhomogeneity of refractive index and can reveal the cellular morphology. These contrasts, together, provide an imaging platform for studying developmental biology, cancer biology, and stem cell biology under an in vivo context. Combined with nanophotonic agents, we have successfully build an in vivo platform for the evaluation of melanoma microenvironment, drug screening, and validation of pharmacokinetics.