The confocal microscope and the lamp microscope are not inherently aligned.  Our hypothesis was that the confocal scanning range was a subset of the lamp microscope range, for the 100x IR objective.

However, by scanning a dried fluorescent sample of 10μm polystyrene, and focusing the lamp view on a unique configuration of particles that were easily identifiable, we found that when the confocal microscope was:

1. Rotated 180 degrees from the intial top position.

2. Zoomed by a factor of 1.8X.

The confocal and lamp views were approximately aligned.  This is confirmed by the corresponding images.

With all three samples at each specific concentration, we found that

The bit values were examined in such a way to ensure that the bit value for the highest pixel value did not exceed the highest