# 3D slicer for confocal microscopy Z stack tiffs

**URL:** <https://discourse.slicer.org/t/3d-slicer-for-confocal-microscopy-z-stack-tiffs/42449>\
**Category:** SlicerMorph\
**Created:** [April 6, 2025, 2:09am UTC](https://discourse.slicer.org/t/3d-slicer-for-confocal-microscopy-z-stack-tiffs/42449 "2025-04-06T02:09:26Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [April 6, 2025, 2:38am UTC](https://discourse.slicer.org/t/3d-slicer-for-confocal-microscopy-z-stack-tiffs/42449/2 "2025-04-06T02:38:41Z")

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> [@Aro\_Nugawela](#):
>
> metadata is the scaling of the images (x=1612 um, y =1612 I’m, z = 817 um with 5um separation between the 163 planes), In tiff format. I have tried importing using slicemorph (following a

This seems to be the physical bounds of the image volume. `ImageStacks` expects you to enter the correct scaling manually. That 1.0x1.0x1.0 is just simply a place holder (it is a common resolution for medical imaging).

So 5 micron (or rather 0.005 as units in Slicer are all mms) seems reasonable given the ROI bounds and the number of slices you reported. But you still need to find out what the resolution in X and Y fields are. In confocal they tend to be much higher resolution than slice spacing. If your metadata does not show you that, then you might be able to get a close enough approximation by dividing the X and Y lengths reported to the X Y image dimension (in pixels). For example if your images are 1024x1024, dividing 1612/1024 will give you the resolution of 1.57 micron/px. Then you can enter this to the XY fields of spacing as 0.00157.

> [@Aro\_Nugawela](#):
>
> (following a YouTube tutorial), but this seems to be scaled to the pixel sizes on the XY and number of planes

I am not sure what tutorial that would be. Official SlicerMorph tutorials are here:

> **[GitHub - SlicerMorph/Tutorials: SlicerMorph module tutorials](https://github.com/SlicerMorph/Tutorials)**
>
> SlicerMorph module tutorials

Specifically [this is the link to the ImageStacks tutorial with some toy microCT data](https://github.com/SlicerMorph/Tutorials/blob/main/ImageStacks/README.md)

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