Hello everyone,
I am working on image-based spatial transcriptomics data Xenium and Merfish. I noticed on several samples of the Xenium data that the transcripts expression coordinate on the x and y axis seems to be shifted depending on the position on the z-axis (see figure). I can see this on all my Xenium samples. I am wondering wether this is due to the shape of the sample, or if this is a bias that should be removed. If any of you knows more on this it would help me !
Thank you very much,
Alexis
It looks like autofocus of the microscope. If you color by FOV you will see that it lines up with the FOV.