Visium

Mouse brain

NCBI719

silver Interactive viewer H&E ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI719_full_image': DataTree[cyx] (3, 8192, 7881), (3, 4096, 3940), (3, 2048, 1970), (3, 1024, 985)
├── Shapes
│     └── 'NCBI719_spots': GeoDataFrame shape: (2735, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2735, 32285)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI719_full_image (Images), NCBI719_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("M1v9WQ5nKljJDdM00000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

Python · lamindb

Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("M1v9WQ5nKljJDdM0")   # stem uid: Lamin resolves it to the 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download M1v9WQ5nKljJDdM00000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/M1v9WQ5nKljJDdM0

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid M1v9WQ5nKljJDdM0

Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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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 (spots): 2,735
Tier: silver
Chemistry: Visium v1
Resolution: 7,881 × 8,192 px
mpp: 1.111 µm/px
Size: 213 MB
Sample ID: NCBI719
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