10x Xenium
Human kidney
GSM9844160
silver Interactive viewer acute tubulointerstitial nephritis No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 10243, 31310), (1, 5121, 15655), (1, 2560, 7827), (1, 1280, 3913), (1, 640, 1956)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (6904, 29790), (3452, 14895), (1726, 7447), (863, 3723), (431, 1861)
│ └── 'nucleus_labels': DataTree[yx] (6869, 29743), (3434, 14871), (1717, 7435), (858, 3717), (429, 1858)
├── Points
│ └── 'transcripts': DataFrame with shape: (4133870, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (12177, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (12177, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (12132, 2) (2D shapes)
└── Tables
└── 'table': AnnData (12177, 5101)
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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("fZh2z0IXd7OzjuXR0000")
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("fZh2z0IXd7OzjuXR") # 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 fZh2z0IXd7OzjuXR0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/fZh2z0IXd7OzjuXR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid fZh2z0IXd7OzjuXRLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Condition
- acute tubulointerstitial nephritis
- Modality
- RNA
- Observations (cells)
- 12,177
- Transcripts
- 4,133,870
- Tier
- silver
- Size
- 279 MB
- Sample ID
- GSM9844160
- License
- NCBI GEO policy
- Published
- Aug 18, 2026
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