# Remove small islands voxel size

**URL:** <https://discourse.slicer.org/t/remove-small-islands-voxel-size/40268>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [November 19, 2024, 4:30pm UTC](https://discourse.slicer.org/t/remove-small-islands-voxel-size/40268 "2024-11-19T16:30:39Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![FraP](https://avatars.discourse-cdn.com/v4/letter/f/e68b1a/32.png) [@FraP](https://discourse.slicer.org/u/FraP)\
**Post date:** [November 19, 2024, 4:30pm UTC](https://discourse.slicer.org/t/remove-small-islands-voxel-size/40268/1 "2024-11-19T16:30:39Z")

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I am using the “Remove Small Islands” function with a voxel size of 10 after segmenting with the threshold function.  
The information of the volume I’m working with is the following:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/3/e32f7f921880c37fb3dffa5bb3b3a260030cd804.png)

Could you confirm if I understand correctly that the voxel size is 0.0004546 mm³?

Thank you for your help!

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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:** [November 19, 2024, 5:30pm UTC](https://discourse.slicer.org/t/remove-small-islands-voxel-size/40268/2 "2024-11-19T17:30:44Z")

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No, that is not correct. Based on the information above, your voxel size is anisotropic. it is 0.00045x0.00045x0.005 (in other words about 0.45 micron in XY and 5 micron in Z axes).

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<div class="post-metadata">

**Author:** ![FraP](https://avatars.discourse-cdn.com/v4/letter/f/e68b1a/32.png) [@FraP](https://discourse.slicer.org/u/FraP)\
**Post date:** [November 20, 2024, 8:05am UTC](https://discourse.slicer.org/t/remove-small-islands-voxel-size/40268/3 "2024-11-20T08:05:46Z")

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Thank you for the answer.

How this applies to the voxel size for “Remove Small Islands” from a segment?  
Does a voxel size of 10 correspond to dimensions of 4.5 × 4.5 × 50 microns?

When I apply it to my segments, this doesn’t seem to be the case. Graphically, it appears to remove only very small islands, around 4.5 microns³.  
Do segments always have isotropic voxels?

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<div class="post-metadata">

**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [November 20, 2024, 9:25am UTC](https://discourse.slicer.org/t/remove-small-islands-voxel-size/40268/4 "2024-11-20T09:25:26Z")

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> [@FraP](#):
>
> Does a voxel size of 10 correspond to dimensions of 4.5 × 4.5 × 50 microns?

Yes.

> [@FraP](#):
>
> When I apply it to my segments, this doesn’t seem to be the case. Graphically, it appears to remove only very small islands, around 4.5 microns³.

This is very hard to confirm visually. If you have any doubts, paint a blob of 10 voxels then one of 9 and see if it’s correct. By the way this part of the code has not changed for about 7 years. Let us know if you do find an issue. (I just tried it and it works as expected)

> [@FraP](#):
>
> Do segments always have isotropic voxels?

No. A segmentation assumes the geometry of its source volume unless you change it manually.