10x Xenium
Human brain
GSM9105223
bronze Interactive viewer glioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27457, 48367), (1, 13728, 24183), (1, 6864, 12091), (1, 3432, 6045), (1, 1716, 3022)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (2085, 2735), (1042, 1367), (521, 683), (260, 341), (130, 170)
│ └── 'nucleus_labels': DataTree[yx] (2068, 2711), (1034, 1355), (517, 677), (258, 338), (129, 169)
├── Points
│ └── 'transcripts': DataFrame with shape: (213274, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (1196, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (1196, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (1221, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1196, 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("3YSYyFdvYUrmwzx00000")
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("3YSYyFdvYUrmwzx0") # 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 3YSYyFdvYUrmwzx00000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3YSYyFdvYUrmwzx0
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3YSYyFdvYUrmwzx0License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- glioma
- Modality
- RNA
- Observations (cells)
- 1,196
- Transcripts
- 213,274
- Tier
- bronze
- Size
- 1.9 GB
- Sample ID
- GSM9105223
- License
- NCBI GEO policy
- Published
- Sep 1, 2025
Cite this dataset
doi.org/10.1016/j.immuni.2025.09.018 ↗ BibTeX
@article{geo:GSM9105223,
doi = {10.1016/j.immuni.2025.09.018},
title = {GSM9105223},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB