A bioreactor includes a base and a lid. The base includes two opposing curved or convoluted surfaces, two opposing flat surfaces, a window disposed on one of the flat surfaces, the window having a higher degree of transparency compared to other portions of the base, wherein images or videos of cells are captured through the window by non-invasive ISM device, and a rounded bottom. The lid is attachable to the base. The lid includes a shaft and a semipermeable membrane attached to the shaft, the semipermeable membrane being permeable to oxygen but impermeable to viruses and bacteria. The PAT-based online analysis directs the adaptive manipulations of bioreactor towards efficient, automated, and GMP-compliant clinical protocols of cell culture.