Why does lowering the condenser make the lamellae more visible?

Lowering the condenser (or alternatively, closing down the iris) causes differences in refractive index across the tissue section to affect the image. When tissues are stained you usually will wish to see only the deposits of dye without interference from the physical properties of the material to which the dye is bound. For unstained material, such as ground sections of bone or tooth, variations in refractive index are all that there is for you to see. Lowering the condenser exaggerates the visual consequences of this variation.

Occasionally it is useful to see the variations in refractive index in stained material. One example is the cross banding pattern of skeletal muscle. Another might be the granules in some marrow slides. A case relevant to ways lab is decalcified bone. The collagen fibers in bone are regularly arranged in directions that change from one lamellae to another. The orientation of the fibers relative to the direction of the light rays can affect the transmission of those rays. So, lowering the condenser may bring out the lamellar patterns of bone, for example Haversian systems. Try it.