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Mouse brain

NCBI717

silver Interactive viewer H&E Provisional
Mouse brain preview
print(sdata) 
SpatialData object
├── Images
│     └── 'NCBI717_full_image': DataTree[cyx] (3, 8192, 7877), (3, 4096, 3938), (3, 2048, 1969), (3, 1024, 984)
├── Shapes
│     └── 'NCBI717_spots': GeoDataFrame shape: (2804, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2804, 32285)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI717_full_image (Images), NCBI717_spots (Shapes)
Load in Python 
import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("8DckCIE4zyQR6RCH")   # latest version

sdata = artifact.load()   # cache, then load into memory
group = artifact.open()   # stream without downloading
path  = artifact.cache()  # sync into the local cache, returns the path
Load from the CLI 
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/8DckCIE4zyQR6RCH

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 8DckCIE4zyQR6RCH
Load with the Python client 
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["8DckCIE4zyQR6RCH0000"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

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Part of collection
Spatial transcriptomics of the mouse brain across three age groups→
6 datasets · comparison

Metadata

Technology
Visium
Organism
mouse
Tissue
brain
Modality
RNA
Observations
2,804
Tier
silver
Chemistry
Visium v1
Resolution
7,877 × 8,192 px
mpp
1.111 µm/px
Size
198 MB
Sample ID
NCBI717
License
CC BY-NC-SA 4.0 NonCommercial
Published
Apr 17, 2023

Cite this dataset

doi.org/10.1016/j.cell.2023.07.027 ↗
BibTeX 
@article{Hahn_2023,
  title = {Atlas of the aging mouse brain reveals white matter as vulnerable foci},
  volume = {186},
  ISSN = {0092-8674},
  url = {http://dx.doi.org/10.1016/j.cell.2023.07.027},
  DOI = {10.1016/j.cell.2023.07.027},
  number = {19},
  journal = {Cell},
  publisher = {Elsevier BV},
  author = {Hahn, Oliver and Foltz, Aulden G. and Atkins, Micaiah and Kedir, Blen and Moran-Losada, Patricia and Guldner, Ian H. and Munson, Christy and Kern, Fabian and Pálovics, Róbert and Lu, Nannan and Zhang, Hui and Kaur, Achint and Hull, Jacob and Huguenard, John R. and Grönke, Sebastian and Lehallier, Benoit and Partridge, Linda and Keller, Andreas and Wyss-Coray, Tony},
  year = {2023},
  month = Sept,
  pages = {4117–4133.e22}
}

Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB