10x Xenium
Mouse liver
GSM8605282
bronze Interactive viewer melanoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23903, 51119), (1, 11951, 25559), (1, 5975, 12779), (1, 2987, 6389), (1, 1493, 3194)
├── Labels
│ └── 'cell_labels': DataTree[yx] (23762, 50766), (11881, 25383), (5940, 12691), (2970, 6345), (1485, 3172)
├── Points
│ └── 'transcripts': DataFrame with shape: (232619, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (189840, 1) (2D shapes)
│ └── 'cell_circles': GeoDataFrame shape: (189840, 2) (2D shapes)
└── Tables
└── 'table': AnnData (189840, 399)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("VsMi55T4HgLi3au50000")
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("VsMi55T4HgLi3au5") # 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 VsMi55T4HgLi3au50000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/VsMi55T4HgLi3au5
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid VsMi55T4HgLi3au5License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- liver
- Condition
- melanoma
- Modality
- RNA
- Observations (cells)
- 189,840
- Transcripts
- 232,619
- Tier
- bronze
- Size
- 1.7 GB
- Sample ID
- GSM8605282
- License
- NCBI GEO policy
- Published
- Jan 14, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB