10x Xenium
Human brain
GSM9105226
bronze Interactive viewer glioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 40983, 42784), (1, 20491, 21392), (1, 10245, 10696), (1, 5122, 5348), (1, 2561, 2674)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (14325, 12463), (7162, 6231), (3581, 3115), (1790, 1557), (895, 778)
│ └── 'nucleus_labels': DataTree[yx] (14319, 12455), (7159, 6227), (3579, 3113), (1789, 1556), (894, 778)
├── Points
│ └── 'transcripts': DataFrame with shape: (817538, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (4736, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (4736, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (4921, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4736, 468)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (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("LB5vfIGYWc9nPOFL0000")
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("LB5vfIGYWc9nPOFL") # 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 LB5vfIGYWc9nPOFL0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/LB5vfIGYWc9nPOFL
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid LB5vfIGYWc9nPOFLLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- glioma
- Modality
- RNA
- Observations (cells)
- 4,736
- Transcripts
- 817,538
- Tier
- bronze
- Size
- 1.7 GB
- Sample ID
- GSM9105226
- License
- NCBI GEO policy
- Published
- Sep 1, 2025
Cite this dataset
doi.org/10.1016/j.immuni.2025.09.018 ↗ BibTeX
@article{geo:GSM9105226,
doi = {10.1016/j.immuni.2025.09.018},
title = {GSM9105226},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB