We are developing a new in-situ spectroscopy tool to observe the birth of morphology: the phase transition during molecular aggregation process. In many systems, molecules self-assemble in ordered fashion such as fibers, helical coils and crystals etc. and manifest interesting properties collectively. One therefore says that morphology is the origin of life and function. The first step of these morphology formation, so-called nucleation, occurs at nano-meter scale and stochastically both in time and space. This stochastic nature has prevented scientists from experimentally observing the event for long time, although understanding this process is critical for rationally designing drugs and materials. We will tackle this problem based on single molecule spectroscopy type approach to achieve the first real-time experimental observation of nucleation, “the birth of morphology”.