[BUG] Registration Warped Incorrectly with Princeton Mouse Brain Atlas

[samclothier]

Describe the bug
I successfully registered the new Princeton mouse brain atlas to our data (1st image), but the output file corresponding to our atlas-registered data appears to have a warped transformation that is misaligned to the atlas (2,3), when using the same command on the same data with the Allen atlas works without issue (4). This issue arises with all datasets tried (currently two).

To Reproduce
Run the following command in the terminal:
brainreg stackDir outputDir -v 5 2 2 --orientation psr --atlas princeton_mouse_20um --n-free-cpus 1
Brainreg executes successfully, but results in data misaligned to the standard atlas.

Expected behaviour
Brainreg successful registration of both the atlas to the data (successful), but most important is registration of the data to the atlas (unsuccessful) for transformation of cell position coordinates into atlas space.

Log file
brainreg_2022-09-06_13-38-00.log

Screenshots

Desktop (please complete the following information):

• OS: Windows
• Version: 21H2
• Hardware specs: 64 GB RAM, Intel Core i5-6600 CPU @ 3.30GHz

Additional context
We just added the Princeton mouse brain atlas to BrainGlobe, and this bug appears to happen only for this new atlas.

[adamltyson]

Hi @samclothier I don't suppose you got anywhere with this issue?

[samclothier]

Hi @adamltyson, unfortunately we didn't figure this out and ended up sticking with the Allen atlas.