10x Xenium
Human kidney
GSM8933093
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 108819, 54194), (1, 54409, 27097), (1, 27204, 13548), (1, 13602, 6774), (1, 6801, 3387)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (106258, 54084), (53129, 27042), (26564, 13521), (13282, 6760), (6641, 3380)
│ └── 'nucleus_labels': DataTree[yx] (106118, 53996), (53059, 26998), (26529, 13499), (13264, 6749), (6632, 3374)
├── Points
│ └── 'transcripts': DataFrame with shape: (20482405, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (317414, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (317414, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (317414, 2) (2D shapes)
└── Tables
└── 'table': AnnData (317414, 480)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("7Spk0u7nSAkJCybB") # 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/7Spk0u7nSAkJCybB
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7Spk0u7nSAkJCybB Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["7Spk0u7nSAkJCybB0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease→ 9 datasets · publication
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Modality
- RNA
- Observations
- 317,414
- Transcripts
- 20,482,405
- Tier
- bronze
- Size
- 5.6 GB
- Sample ID
- GSM8933093
- License
- NCBI GEO policy
- Published
- May 30, 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