Add dorr_mouse_mri atlas

[saarah815]

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Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

What does this PR do?

Add Dorr mouse MRI atlas to Brainglobe API.

Does this PR require an update to the documentation?

Yes.

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[IgorTatarnikov]

I think you're working off of an old version of main, could you pull the most recent version of main and rebase or merge it into this branch?

We're now storing atlas generation scripts in a separate directory in the root of the repository, and the imsave -> imwrite bug fix is already present along with support for multi-threading for mesh generation.

[saarah815]

Thanks @IgorTatarnikov - explains why pre-commit is working now! I've just pushed again.

[IgorTatarnikov]

I've tried the packaging and it works great! I've left a few comments in terms of code style.

One outstanding question is how to handle L/R labels. BrainGlobe doesn't typically use separate annotation labels for L/R of the same structure, we use the hemisphere array to differentiate between left and right. @adamltyson @alessandrofelder do you know how we've handled atlases with separate left/right annotations in the past?

[saarah815]

Thank you @IgorTatarnikov @adamltyson @alessandrofelder! Just pushed with the merged annotations and other formatting fixes. Used the same approach as the axolotl atlas.

[IgorTatarnikov]

Thanks for making the changes.

I've generated the atlas and it looks great!

However, there are duplications in the region abbreviation names. For example, both the Hippocampus and the Hypothalamus are abbreviated as H, Medulla and Midbrain as M.

Not sure what's best to do in this case, you could use the a similar approach as you've done now (first capital letters of all regions) with a fallback to make sure there's at least 3 letters in the acronym, or keep track of acronyms already used and add a letter if it's not unique 🤔 You could also use the Allen mouse ontology as a guide but that may require some fuzzy matching, as not all regions described in this atlas have an equivalently named structure in the Allen.

[saarah815]

Ah I see, my bad! Let me change that to avoid duplicates :)

[IgorTatarnikov]

Looks great! I think this is good to go. I'll upload the packaged atlas to GIN and update the last_versions.conf file.

The next steps are:

• Update the table on the website, and the atlas details page.
• Add a quick blog post about the new atlas
• Update the README.md for this repo

We can open up issues in the appropriate repos to track the outstanding tasks.

[IgorTatarnikov]

The atlas is now available via the brainglobe-atlasapi. I've visualised the uploaded version and all seems in order! Merging this now as everything is now tracked via issues.