10x Xenium
Mouse brain
GSM8605279
bronze Interactive viewer melanoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 34136, 53961), (1, 17068, 26980), (1, 8534, 13490), (1, 4267, 6745), (1, 2133, 3372)
├── Labels
│ └── 'cell_labels': DataTree[yx] (34083, 53960), (17041, 26980), (8520, 13490), (4260, 6745), (2130, 3372)
├── Points
│ └── 'transcripts': DataFrame with shape: (13247851, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (163281, 1) (2D shapes)
│ └── 'cell_circles': GeoDataFrame shape: (163281, 2) (2D shapes)
└── Tables
└── 'table': AnnData (163281, 399)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("pbU32GDirPYD0e87") # 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/pbU32GDirPYD0e87
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pbU32GDirPYD0e87 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["pbU32GDirPYD0e870000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Condition
- melanoma
- Modality
- RNA
- Observations
- 163,281
- Transcripts
- 13,247,851
- Tier
- bronze
- Size
- 3.0 GB
- Sample ID
- GSM8605279
- License
- unknown
- Published
- Jan 14, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB