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kim mouse atlas meshes are scaled incorrectly #247

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adamltyson opened this issue Dec 7, 2020 · 4 comments
Closed

kim mouse atlas meshes are scaled incorrectly #247

adamltyson opened this issue Dec 7, 2020 · 4 comments
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atlasgen Issue was transferred from the retired bg-atlasgen. Concerns the atlas_generation submodule.

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@adamltyson
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I think each set of meshes is consistent, but they are scaled incorrectly, so they don't play nicely with external data.

@adamltyson adamltyson self-assigned this Dec 7, 2020
@FedeClaudi
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I think you're right...

image

in red is the allen atlas, in transparent kim 100um.
To reproduce:

from brainrender import Scene


s = Scene(atlas_name='kim_mouse_100um')

s2 = Scene()

s2.root.c('red').alpha(1)
s.add(s2.root)
s.render()

@FedeClaudi
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In blue is kim 50um, that seems to be the same as the allen_mouse_25um
image

@vigji
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vigji commented Dec 8, 2020

There is an argument in the wrap_up utility function that should change if meshes are specified in pixels or microns to decide whether to scale them or not (convention for the final meshes is in microns). Maybe the problem's there?

@adamltyson adamltyson removed their assignment Feb 14, 2022
@adamltyson adamltyson transferred this issue from brainglobe/brainglobe-atlasapi Sep 19, 2023
@willGraham01 willGraham01 added the atlasgen Issue was transferred from the retired bg-atlasgen. Concerns the atlas_generation submodule. label Feb 23, 2024
@willGraham01 willGraham01 transferred this issue from brainglobe/bg-atlasgen Feb 23, 2024
@alessandrofelder
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Closed by #271

@github-project-automation github-project-automation bot moved this from Backlog to Done in Core development May 9, 2024
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Labels
atlasgen Issue was transferred from the retired bg-atlasgen. Concerns the atlas_generation submodule.
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5 participants