Accessing full resolution region segmentations for Mouse, P56, Sagittal atlas

1

Hi, I’m trying to download region segmentations for the Mouse, P56, Sagittal atlas using the Allen image download API . However, the images downloaded via the API seem to have region segmentations at a much lower detail than available on the online viewer (e.g. in attached images- the layers in CTX are not differentiated in the downloaded image/left but can be seen in the online viewer/right). Might there be a way to access the region segmentation data for this atlas at the level of detail seen in the viewer? Would appreciate any pointers. Thanks you!

Screenshot 2025-12-02 at 10.33.31 AM
Screenshot 2025-12-02 at 10.33.31 AM1298×414 302 KB

2

Do you mind sharing the code you used to download the image on the left? That would provide a good starting point for us to figure out how to get you unblocked.

Thanks.

3

I was able to resolve this and see the region boundaries by just using a different svg viewer (Inkscape instead of Acorn).

Also, adding the code here in case it’s helpful for anyone else:

from allensdk.api.queries.image_download_api import ImageDownloadApi
from allensdk.api.queries.svg_api import SvgApi
from allensdk.config.manifest import Manifest

from allensdk.api.queries.image_download_api import ImageDownloadApi
import pandas as pd

image_api = ImageDownloadApi()
atlas_id = 2  # P56 Mouse Brain Atlas
atlas_image_records = image_api.atlas_image_query(atlas_id)
atlas_image_dataframe = pd.DataFrame(atlas_image_records)

sagittal_ids = atlas_image_dataframe[‘id’].tolist()
sagittal_id = sagittal_ids[0]

downsample = 0  # 0 = full resolution

svg_api = SvgApi()
file_path = f’./{sagittal_id}_svg.svg’
svg_api.download_svg(sagittal_id, file_path=f’{file_path}')

Thanks!

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