Optimizing Autofocus¶

Focus, Z Focus, tomo Focus and other variation of focus nodes use the same Focus class but with different settings, focus sequence and position in the MSI sequence to achieve different effects. Each need to be optimized for your instrument and usage. The defaults we provide works for us but an understanding of how it works can help you having the smoothest run and getting the best data.

Node Name	Found in Application	Prerequisite	Performance Target
Z Focus	all MSI	visible area on the grid	grid almost at eucentric height, defocus zero is no more than what Focus node can handle
Focus	most MSI	grid almost at eucentric height to allow using only defocus to make correction without significant beam shift	defocus zero is reset to within acceptable tolerance for final exposure
Tomo Focus	MSI-Tomography	grid close to eucentric height, defocus zero is at eucentric height	grid is accurately set at eucentric height

What you should see during autofocus by beam tilt:¶

Here is an 512x512 example image pair acquired in Focus node at 0.14 nm/pixel at beam tilt separated by 0.8 mrad:

focus1 image	focus2 image

At Focus node of your MSI application, you can watch their display. Make sure that beam has not shift off the view (an indication of be Beam Tilt Pivot Point Alignment) and the contrast does not reverse (Objective aperture not centered or too small for the beam tilt applied).

In the same node, you can make it display the correlation like this:

The correlation map shown in Leginon has origin (identical image correlation) at top left corner and is wrapped around so that peaks close to all corners means smaller shift than peaks close to the center of the correlation map. In this example, phase correlation is used, and focus2 is shifted from focus1 to the top-left by a distance of about 1/15 of the image. Therefore, we see a peak at bottom-right. and the phase correlation peak is sharp and with modulations around it.

You may notice that the peak is elongated. This is caused by the coma effect of the beam tilt.

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