Z-Stack Scanning - Leica Aperio AT2 DX User Manual

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First, place the slide tray into load position by clicking the Eject button at the bottom of the Console window.

Place the slide on the stage with the coverslip up and the label oriented to the front.

Take a snapshot to get a macro image of the slide by clicking the Snapshot button.

After the snapshot is taken, you see the macro image of the slide in the window.

Set at least four focus points, preferably more. You can click the Auto Select Focus Points icon

scanner to automatically set focus points.

Click the Capture a calibration image icon.

The focus points turn green as they are focused.

A calibration image is taken. When the calibration operation is complete, the calibration image appears.

The calibration image should be consistent with non-tissue areas of a slide, typically light gray. (The illustration above

shows a good calibration image.)

If the calibration image is too dark or displays shadowing, the light may need replacing. If the calibration image shows

tissue, move the blue diamond calibration point out of the tissue area and make a new calibration image.

Z-Stack Scanning

The Aperio AT2 DX can create multiple digital images of slide tissue scanned at different focal depths, creating a 3D image

that you can visually navigate through much as a microscope user can navigate through different tissue focal depths by

using the microscope objective fine and coarse adjustments. This ability to create a 3D image is called "z-stack scanning."

Use z-stack settings to scan a single slide as a z-stack, or save those settings as a permanent slide setting that can be used

to scan groups of slides as z-stacks in the future. You can create z-stack scan settings for a manually scanned slide that is

under the objective or for a slide in a scan batch.

For all types of scanning, the Aperio scanner determines the layer within the tissue that provides the optimal focus—this is

called the best focus layer. For z-stack scanning, by default the best focus layer is placed in the middle of the z-stack, with

an equal number of layers above and below it.

To configure a z-stack scan:

Chapter 4: Scanning Slides

to tell the

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