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brainglobe / brainglobe-atlasapi

A lightweight python module to interact with atlases for systems neuroscience
https://brainglobe.info/documentation/brainglobe-atlasapi/index.html
BSD 3-Clause "New" or "Revised" License
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perens_atlas alignment trouble with new version [BUG] #281

Closed pr4deepr closed 1 month ago

pr4deepr commented 1 month ago

Hi I have been registering my LSFM dataset to the perens atlas and it has been working well until the latest update to the atlas (1.1). When I checked the registration it was quite warped and looked out of proportion.

Alignment results before update: image

After update: image

I just used the check orientation option in the brainerender plugin and I get this:

image

The orientation of my dataset is sal .

Also, is it possible to roll back to the previous version of an atlas?

Cheers Pradeep

adamltyson commented 1 month ago

Hi @pr4deepr, sorry about this, the new version seems to have been oriented incorrectly. We don't provide a way to easily roll back I'm afraid, but you can download any version of the atlas you need from here, untar it and place it in your ~/.brainglobe directory (then make sure to not update, at least until we've fixed this).

I will close this issue, but I've raised https://github.com/brainglobe/brainglobe-atlasapi/issues/282 to track.

pr4deepr commented 1 month ago

Thanks @adamltyson for the links to the atlases. Hope you're doing well..

adamltyson commented 1 month ago

I'm good thanks @pr4deepr, hope all is well in Melbourne!

The orientation of this atlas should be fixed now. When you get a minute, would you mind testing your pipeline with the latest version (1.2)?

pr4deepr commented 1 month ago

Thanks a lot. Its working now..