This chapter serves as an illustration of how and what is happening for z alignment in ZEN Connect. Consider the following situation:

This image illustrates two z-stacks with five planes and different z coordinates (with µm as unit). The green line simulates the position of the Global-Z slider. Here, the Correlative Workspace would show you plane 1 of the first stack and an empty frame where the second stack would be because the Global-Z is beyond the range of the second stack.

Aligning Stack 2 in z direction

Now the second stack is aligned according to the workflow described in Aligning Images in Z Direction with a Relative Z Offset of 3µm. The result then is the following:

All z planes of Stack 2 are shifted by 3µm and now the z-plane 1 of Stack 1 and z-plane 3 of Stack 2 would be visible in the Correlative Workspace.

Aligning the whole session in z direction

Now the whole session with both images is shifted with a Relative Z Offset of 4µm.

Now the first stack is out of range of the Global-Z slider, so the Correlative Workspace would show you plane 1 of Stack 2 and an empty frame where Stack 1 is located.