10x Xenium

Human pleura

GSM9052321

bronze Interactive viewer pleural mesothelioma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Labels
│     ├── 'cell_labels': DataTree[yx] (50403, 34802), (25201, 17401), (12600, 8700), (6300, 4350), (3150, 2175)
│     └── 'nucleus_labels': DataTree[yx] (50262, 34664), (25131, 17332), (12565, 8666), (6282, 4333), (3141, 2166)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (86150, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (86150, 2) (2D shapes)
│     └── 'nucleus_boundaries': GeoDataFrame shape: (86150, 1) (2D shapes)
└── Tables
      └── 'table': AnnData (86150, 339)
with coordinate systems:
    ▸ 'global', with elements:
        cell_labels (Labels), nucleus_labels (Labels), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("ZY5xEAVMnrGBmoqf0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("ZY5xEAVMnrGBmoqf")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download ZY5xEAVMnrGBmoqf0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ZY5xEAVMnrGBmoqf

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ZY5xEAVMnrGBmoqf

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Metadata

Technology: 10x Xenium
Organism: human
Tissue: pleura
Condition: pleural mesothelioma
Modality: RNA
Observations (cells): 86,150
Tier: bronze
Size: 117 MB
Sample ID: GSM9052321
License: NCBI GEO policy
Published: Jun 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