Multiphoton microscopy enables the 3D visualisation of large sections of biological tissues to understand the relationship between their structure and function, leading to applications in biomedicine and drug delivery. The EU-funded Micro4Nano project aims to develop methods for 3D visualisation up to 1 mm in depth, combining hyperspectral imaging of autofluorescent species with structural information from second-harmonic generation signals and multifunctional fluorescent labels as well as chemical information from Raman microscopy. A new generation of multifunctional nanocarriers for two-photon microscopy and drug delivery will be designed for real-time monitoring of living cells and tissues. The network training programme offers career development opportunities for early-career scientists and fosters the interdisciplinary collaboration between participant organisations.