napari shows a mirror image of your tomogram

[GavinR1]

I believe Napari-boxmanager is reflecting tomograms along the Y-axis resulting in a mirrored image of what's actually in the tomogram.

Here's an example:

on the the left is a micrograph from the tilt series and on the right is a slice from the imod reconstruction visualized with imod. I had to rotate the tomogram 180 degrees along the Y-axis to make it match what's in the tilt series but no reflection is necessary.

Here's the same tomographic slice shown in napari. Note that the y-axis is reflected compared to the original micrograph.

As a result, any cellular structures would be shown as a mirror image which could lead to confusion.

I just loaded a finder grid into the krios and will check whether the handedness is in fact correct in the original micrograph. Assuming it is, we should change the boxmanager to display the correct handedness.