10x Xenium
Human kidney
xenium-protein-ffpe-human-renal-ccrcc
silver Interactive viewer clear cell renal carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (35, 54535, 54059), (35, 27267, 27029), (35, 13633, 13514), (35, 6816, 6757), (35, 3408, 3378)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (54535, 54059), (27267, 27029), (13633, 13514), (6816, 6757), (3408, 3378)
│ └── 'nucleus_labels': DataTree[yx] (54535, 54059), (27267, 27029), (13633, 13514), (6816, 6757), (3408, 3378)
├── Points
│ └── 'transcripts': DataFrame with shape: (75544755, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (690322, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (690322, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (697966, 2) (2D shapes)
└── Tables
└── 'table': AnnData (690322, 477)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (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("FnIc5OeVSwfbshQS0000")
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("FnIc5OeVSwfbshQS") # 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 FnIc5OeVSwfbshQS0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/FnIc5OeVSwfbshQS
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid FnIc5OeVSwfbshQSLicense: CC BY 4.0
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- kidney
- Condition
- clear cell renal carcinoma
- Modality
- RNA
- Observations (cells)
- 690,322
- Transcripts
- 75,544,755
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 65.3 GB
- Sample ID
- xenium-protein-ffpe-human-renal-ccrcc
- License
- CC BY 4.0
- Published
- Aug 19, 2026
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB