Before you perform automatic configuration, the current focus position has to be at the center of the sample. The camera's current field of view must always be at a position on the sample that shows a signal in the selected channel.
Automatic z-stack configuration only works with microscopes and systems that do not use an optical sectioning technique. If you use an LSM, ApoTome, VivaTome, Spinning Disc (CSU) or another technique for generating optical sections, the z-stack has to be configured manually.
- Make sure that you have placed a sample in the visual field of the camera and that the sample is roughly in focus. Set the exposure time of the camera fair enough for receiving a good signal.
- On the Acquisition tab, in the Z-Stack tool, click Start Auto Configuration.
- Confirm the system message by clicking OK.
- The automatic configuration starts. The auto configuration can last for a few seconds up to half a minute depending on the acquisition settings. You can check the status on the Progress bar in the Status bar.
- The auto configuration sets the focus position for the first, last and center slice of the z-stack, the number of slices and the interval automatically. The z-stack experiment is set up successfully now.
- Click Start Experiment to start the experiment.
- You have successfully set up and performed an z-stack experiment.
You can change the area of the sample (z direction in %) covered by the z-stack auto configuration under Tools > Options > Acquisition > Z-Stack. Smaller values enlarge the z-stack, higher values make the z-stack smaller.