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Australian mouse brain #409

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PolarBean
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This is to add the australian mouse brain atlas, resolving this issue.
#319
The benefits of this atlas are that it is a 15µm resolution MRI template. Which I believe is currently the highest resolution MRI template by quite a distance (Though they used a novel method to upsample from 30µm described here: https://cds.ismrm.org/protected/12MProceedings/PDFfiles/1077.pdf.)
Also these annotations are at least partially based on the Paxinos ontology and Paxinos is an author which may be useful for comparative purposes as the Paxinos atlas is widely used for 2D atlasing.
The challenges when adding this atlas that I faced were the following:

  • The annotations were stored across multiple files with multiple corresponding label metadata
  • The IDs were overlapping between files which required renumbering to resolve
  • The acronyms for each ID were given but for the full name I had to search for tables in the corresponding paper for that region.
  • The acronym to full name tables were formatted differently in different journals, in one case it was a png. This is why I had to include the JSON that I constructed in the atlas generation script here.
  • In some limited cases it wasnt entirely clear which full name an acronym corresponded to which required me making an educated guess. Some were obvious, others less so.

Nonetheless, hopefully this is a useful addition to the API.

@adamltyson
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Thanks @PolarBean! Bear with us, it might be a few days until we can review this.

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