10x Xenium
Mouse brain
GSM9039188
bronze Interactive viewer diffuse midline glioma, H3 K27-altered Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 51109, 54036), (4, 25554, 27018), (4, 12777, 13509), (4, 6388, 6754), (4, 3194, 3377)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (50606, 53916), (25303, 26958), (12651, 13479), (6325, 6739), (3162, 3369)
│ └── 'nucleus_labels': DataTree[yx] (50283, 53380), (25141, 26690), (12570, 13345), (6285, 6672), (3142, 3336)
├── Points
│ └── 'transcripts': DataFrame with shape: (296287748, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (226967, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (226967, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (225772, 2) (2D shapes)
└── Tables
└── 'table': AnnData (226967, 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("3h6ekgZ2Ts9fy8W50000")
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("3h6ekgZ2Ts9fy8W5") # 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 3h6ekgZ2Ts9fy8W50000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3h6ekgZ2Ts9fy8W5
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3h6ekgZ2Ts9fy8W5License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Condition
- diffuse midline glioma, H3 K27-altered
- Modality
- RNA
- Observations (cells)
- 226,967
- Transcripts
- 296,287,748
- Tier
- bronze
- Size
- 18.4 GB
- Sample ID
- GSM9039188
- License
- NCBI GEO policy
- Published
- Dec 22, 2025
Cite this dataset
doi.org/10.1126/scitranslmed.adr1557 ↗ BibTeX
@article{geo:GSM9039188,
doi = {10.1126/scitranslmed.adr1557},
title = {GSM9039188},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB