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Hemisphere improvements to axolotl atlas #438

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merged 3 commits into from
Dec 13, 2024
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alessandrofelder
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Description

What is this PR

  • Bug fix
  • Addition of a new feature
  • Other

Why is this PR needed?
The UNAM axolotl atlas is asymmetric and has duplicate region acronyms (because the same region exists in each hemisphere)

What does this PR do?

  • Computes and adds the (asymmetric) hemisphere stack for the axolotl atlas
  • distinguishes duplicate region acronyms by labelling them L or R

References

First tickbox of #359
Closes #437

How has this PR been tested?

Visual inspection and validation script on local axolotl atlas.

Is this a breaking change?

No

Does this PR require an update to the documentation?

No

@alessandrofelder alessandrofelder requested a review from a team December 6, 2024 14:46
@adamltyson
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distinguishes duplicate region acronyms by labelling them L or R

Do we need this? The whole point of the hemispheres stack is so that we don't have seperate regions for L & R.

@alessandrofelder
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alessandrofelder commented Dec 6, 2024

We need this for PinPoint (#437), which requires unique acronyms. The alternative would be to merge annotation regions in the atlas, but would mean deviating from the original data?

@adamltyson
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adamltyson commented Dec 6, 2024

All our other atlases have the same region (and acronym) in L & R hemispheres. The hemisphere is then encoded by the image.

Does this atlas have different numerical IDs in each hemisphere? If so, this is what should be corrected to meet the BrainGlobe spec.

@alessandrofelder
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Does this atlas have different numerical IDs in each hemisphere?

Yep, it does.

Does this atlas have different numerical IDs in each hemisphere? If so, this is what should be corrected to meet the BrainGlobe spec.

OK!

@adamltyson
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I guess this should be added to the list of things that need to be documented 😞

@alessandrofelder
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alessandrofelder commented Dec 12, 2024

I guess this should be added to the list of things that need to be documented

#438

I've addressed the comments, and think this is ready now :)

@adamltyson adamltyson merged commit 9b5d20f into main Dec 13, 2024
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@adamltyson adamltyson deleted the axolotl-improvements branch December 13, 2024 10:52
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[BUG] Duplicate entries in acronyms in axolotl atlas?
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