Biology & Biochemistry Imaging Core (BBIC)

In case of Z-stack trouble while in MATL mode

While clicking the “depth” button BEFORE setting matrix coordinates should enable the program to scan in an XYZ mode, we have occasionally experienced problems with a lack of Z- stacking. If you experience this problem, here is a software backdoor to correct it.

If the MATL program is recognizing Z-axis settings, you should see the Z indicator in the bottom left corner (red arrow) of the Registered Point List window.

matl-z-trbsht

If you do not see this Z indicator after you click start, stop the scan and right-click on the 1st line of the Registered Point List. Choose “Edit Acquisition Parameters”:

matl-z-trbsht-1

This opens the TC [Imaging setting] window:

matl-z-trbsht-2

This example shows how the window should look if the XYZ mode is enabled (cyan arrow and “*”). If the Z axis is not recognized, you will see this:

matl-z-trbsht-3

To correct the problem, click the “Depth” button, then the “OK” button at the bottom right of the window. Do this for each point listed on the registered point list. That should make the program do an XYZ scan for each tile.

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