About The Z-Stack Scanning Window; Basic Z-Stack Settings - Leica Aperio AT2 DX User Manual

Chapter 4: Scanning Slides
1. First, take a snapshot of a slide (see "Using Snapshots" on page 28).
2.
Open the slide in the slide view window.
3. Click the icon in the Manual Setup section of the slide view window.
You see the Z-Stack Scanning window.

About the Z-Stack Scanning Window

The Z-Stack Scanning Window allows you to do several different things:
1. Make simple settings for z-stack scanning using the controls on the window. After making those settings, you will
click the Apply button, click the red X at the top of the window to close it, then click the Scan button on the slide
view window to scan the slide with these settings. See "Basic Z-Stack Settings" below for more.
2. Refine z-stack scanning settings by using the Advanced Z-Stack Options control. This allows you to set layer
offsets. See "Advanced Z-Stack Settings" below for more.
3.
Save the z-stack settings you have made as a slide setting to use in the future on other slides by clicking the
Create button. See "Saving Z-Stack Settings as a Slide Setting" on page 33.
For a visual reminder of how the z-stack layers are arranged and for tips on using the controls, hover over the Info icon in
either the basic or the advanced configuration sections.

Basic Z-Stack Settings

Configure the basic z-stack scan settings by telling the scanner how many focal layers you want to scan and the distance
between the layers in microns. For example, if you configure the z-stack to use 5 layers separated by .5 microns, there are
two layers above the best focus layer and two layers below it.
1.
Select the number of layers by clicking up and down arrows in the Layers box. Select the number of layers based
on the thickness of the sample.
2. Adjust the separation between the layers by clicking the up and down arrows in the Layer Separation box. This
controls the focus offset between layers.
3.
When satisfied with the settings, click Apply to apply the settings to the current slide and click the red X at the top
of the window to close it.
4.
Click Scan on the slide view window to scan the slide.
32 Aperio AT2 DX User's Guide, Revision B © Leica Biosystems Imaging, Inc. 2020