In Pixels:The size is fixed and the same for all markers; zooming in or out has no effect on the display size of the markers. This is the usual method for displaying markers.
In Microns: The size of the markers is the same for all markers and is adjusted as you zoom. The markers are scaled along with the tracing.
Intrinsic: The intrinsic size for each marker is defined by the diameter of the circular cursor when the marker was placed; therefore the intrisic value cannot be modified in 3D. Since this size is defined in actual micrometers, the displayed size depends on the zoom level. If you zoom out, you may not see the markers since they are scaled as small as possible. The intrinsic setting allows you to define a different size for each marker.