Visium
Mouse brain
NCBI808
bronze Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI808_full_image': DataTree[cyx] (3, 11266, 11446), (3, 5633, 5723), (3, 2816, 2861), (3, 1408, 1430)
├── Shapes
│ └── 'NCBI808_spots': GeoDataFrame shape: (2359, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2359, 32285)
with coordinate systems:
▸ 'global', with elements:
NCBI808_full_image (Images), NCBI808_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("G85IpeSC3eK9HSTn0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("G85IpeSC3eK9HSTn") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download G85IpeSC3eK9HSTn0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/G85IpeSC3eK9HSTn
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid G85IpeSC3eK9HSTnLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
Regional differential gene expression analyses of brains from four 24w-old Nf1+- mice→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,359
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 11,446 × 11,266 px
- mpp
- 0.761 µm/px
- Size
- 333 MB
- Sample ID
- NCBI808
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Apr 5, 2024
Cite this dataset
No linked publication found — please cite the data source.
License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB