The microscope has its limitations. And when you get into the scanning electron microscopes for examining the nature of the atom, you find that their beams of electrons interact with the atoms being observed, impacting the nature of the atom itself. And it must focus on an object, not the empty space that surrounds each component of the atom.
But the soul is not physical. It cannot be measured or timed or dissected or even observed. It is felt. Therein lies the limitation of Science when it comes to proving what is real but intangible.
Scientists may be able to observe areas of the brain that “light up” when people are in deep meditative states of bliss. They may be able to record the Alpha waves of a spiritual master. But they will never be able to grasp the soul. They do not have the correct instruments for this and never will.
And yet, quantum physics is bringing us closer to the realization that the forces that govern the entire Universe are unseen and lie outside all the physical senses. In that sense, Science will eventually accept the existence of the Soul but will not be able to prove it.