In the field of biophotonics the main goals are the control and processing of in vivo biological tissues and the monitoring of biomolecule dynamics. Two particular “pitfalls” are present: the dynamic multiscale organization and the photostress of the medium. Until now the state of the art of the pico-femtosecond systems designed to these applications shows that the changing laser technology has been only used as an add-on. Our approach is based on a bottom-up procedure and on the medium-centered knowledge. The range of neurobiological applications of ultrafast photonics extends from TRP (time-resolved propagation) to linear and non-linear TRE (time-resolved emission). The device combines a one kilohertz chirp pulse amplification laser system and a single shot streak camera. For discrete wavelength applications (TRE), the set-up is a SHG/OPG/OPA3/SHG design. In the case of TRP, the beam is focused into pure water to generate a white light continuum. After propagation through tissue, a single-shot streak camera with single photo-electron counting capability performs the picosecond time-resolved spectroscopy of the collected photons. Depending on the acceptable level of photostress, the integration time can extend from 33ms up to several minutes with a real-time control of the jitter and time drifts. The meaning of the TRE spectro-temporal image is particularly detailed in the 450-480nm excitation window in regards to the contributions of mitochondrial flavoproteins. This optical system fulfills the reliability and the sensitivity, conditions required for measuring opto-electronic quantities from freely moving animal at low irradiation.