# Xenium z-coord normalization

**URL:** <https://discourse.scverse.org/t/xenium-z-coord-normalization/3347>\
**Category:** spatialdata\
**Created:** [November 19, 2024, 11:53am UTC](https://discourse.scverse.org/t/xenium-z-coord-normalization/3347 "2024-11-19T11:53:31Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![alexis](https://avatars.discourse-cdn.com/v4/letter/a/838e76/32.png) [@alexis](https://discourse.scverse.org/u/alexis)\
**Post date:** [November 19, 2024, 11:53am UTC](https://discourse.scverse.org/t/xenium-z-coord-normalization/3347/1 "2024-11-19T11:53:31Z")

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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

 ![Screenshot from 2024-11-19 12-47-03](https://canada1.discourse-cdn.com/flex035/uploads/forum11/original/2X/6/6c631bf269af35414c2e969d1c326b3ff26d5c93.png)

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**Author:** ![cane11](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/cane11/32/241_2.png) [@cane11](https://discourse.scverse.org/u/cane11)\
**Post date:** [November 19, 2024, 5:27pm UTC](https://discourse.scverse.org/t/xenium-z-coord-normalization/3347/2 "2024-11-19T17:27:18Z")

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It looks like autofocus of the microscope. If you color by FOV you will see that it lines up with the FOV.