10x Xenium
Mouse brain
GSM9039189
bronze Interactive viewer diffuse midline glioma, H3 K27-altered Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 54508, 54052), (4, 27254, 27026), (4, 13627, 13513), (4, 6813, 6756), (4, 3406, 3378)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (54263, 53850), (27131, 26925), (13565, 13462), (6782, 6731), (3391, 3365)
│ └── 'nucleus_labels': DataTree[yx] (52994, 53750), (26497, 26875), (13248, 13437), (6624, 6718), (3312, 3359)
├── Points
│ └── 'transcripts': DataFrame with shape: (288646298, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (210460, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (210460, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (208932, 2) (2D shapes)
└── Tables
└── 'table': AnnData (210460, 5006)
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("iRVyAGTjHmSdwdUa0000")
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("iRVyAGTjHmSdwdUa") # 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 iRVyAGTjHmSdwdUa0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/iRVyAGTjHmSdwdUa
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid iRVyAGTjHmSdwdUaLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Condition
- diffuse midline glioma, H3 K27-altered
- Modality
- RNA
- Observations (cells)
- 210,460
- Transcripts
- 288,646,298
- Tier
- bronze
- Size
- 18.4 GB
- Sample ID
- GSM9039189
- License
- NCBI GEO policy
- Published
- Dec 22, 2025
Cite this dataset
doi.org/10.1126/scitranslmed.adr1557 ↗ BibTeX
@article{geo:GSM9039189,
doi = {10.1126/scitranslmed.adr1557},
title = {GSM9039189},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB