Those crystals are most likely kyber crystals. Yoda says that the planet is strong with the Force and he feels, and sees, the strong amount of life emanating from inside the planet. Kyber crystals resonate with the Force, and there is a lot of Force to resonate with at this planet.
Also kyber crystals are composed of both inorganic and organic material. Since there is a vast amount of organic material inside the planet, its not too far fetched that some of the organic matter helps to make the crystals.
One more note that reinforces that they are kyber crystals is that fact that the light that glows within each crystal fade in and out. Since the glow isn't from an outside light source its possibly a way to show their almost sentience, and them reacting to the Force emanating from inside the planet.