10x Xenium
Human brain
GSM9054423
bronze Interactive viewer ependymoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 30646, 39753), (1, 15323, 19876), (1, 7661, 9938), (1, 3830, 4969), (1, 1915, 2484)
├── Points
│ └── 'transcripts': DataFrame with shape: (50844823, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (144901, 2) (2D shapes)
└── Tables
└── 'table': AnnData (144901, 366)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("mD2hNiHed0M79cS20000")
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("mD2hNiHed0M79cS2") # 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 mD2hNiHed0M79cS20000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/mD2hNiHed0M79cS2
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid mD2hNiHed0M79cS2License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- ependymoma
- Modality
- RNA
- Observations (cells)
- 144,901
- Transcripts
- 50,844,823
- Tier
- bronze
- Size
- 3.0 GB
- Sample ID
- GSM9054423
- License
- NCBI GEO policy
- Published
- Dec 9, 2025
Cite this dataset
doi.org/10.1038/s41586-026-10214-2 ↗ BibTeX
@article{geo:GSM9054423,
doi = {10.1038/s41586-026-10214-2},
title = {GSM9054423},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB