# Creating meshes from volumetric data

**URL:** <https://community.brain-map.org/t/creating-meshes-from-volumetric-data/509>\
**Category:** Technical\
**Tags:** reference-coordinates, annotation, anatomy, how-to, atlas-reference-maps, allensdk\
**Created:** [April 12, 2020, 10:21pm UTC](https://community.brain-map.org/t/creating-meshes-from-volumetric-data/509 "2020-04-12T22:21:17Z")\
**Posts on this page:** 1\
**Showing post:** 5

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**Author:** ![anorak](https://avatars.discourse-cdn.com/v4/letter/a/e9bcb4/32.png) [@anorak](https://community.brain-map.org/u/anorak)\
**Post date:** [June 28, 2020, 12:07am UTC](https://community.brain-map.org/t/creating-meshes-from-volumetric-data/509/5 "2020-06-28T00:07:34Z")

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Hi Lydia

Thanks for your reply. Sorry for getting back so late, i was doing other stuff for my thesis. By Volumetric data i mean the 3D reference atlas which for the p4 is 724x403x398 with 398 sagittal sections. Yes i am asking about the reference atlas.

I am drawing annotations on 40 sections out of 398 and then interpolating it to get structure masks for all slices. I then do an export mesh in itk-snap. I went through the paper you linked and the new system seems too complex for a single person to do it on his own.

I was wondering if you could give me some tips on whats missing in my workflow or how to improve it. i am happy if i manage to even get the quality of allen brain mesh v1

 ![Screenshot 2020-06-28 at 02.05.20](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/c93073f356ddabc9316d325376090ef82903518b.png) ![Screenshot 2020-06-28 at 02.00.28](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/76fc1075b5f904c5e2177b4df71b4110c0d114d5.png)

As you can see there are a lot of microtears in my meshes. and i dont know how to go about fixing that

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