I am using micro-manager to control a Zeiss Axio Observer Z1 microscope. We currently have a marzhauser motorized stage on the scope. I've been able to use multi-D acquisition to acquire images at multiple positions in a single z-plane using Definite Focus to maintain focus over time. However, I'm experiencing issues when I try to acquire z-stacks at a single position. I tried setting positions above and below the plane in which the sample is in focus, however, when I try to capture the z-stack, it takes images at the last position for all slices i.e. if I select a 10 slice z-stack, all 10 slices will be identical. Can anyone provide any assistance on remedying this situation? I tried to look for older posts with a similar issue, but wasn't able to find a resolution.
I had the same issue when I started off with using Z-Stacks on our Nikon Scope. Troubleshooting the issue I found that the Z-Device was not configured in the micromanager configuration. I'm not entirely sure how it is for Zeiss, but I'm pretty sure its something similar.