10x Xenium
Human brain
GSM9105221
bronze Interactive viewer glioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27491, 39964), (1, 13745, 19982), (1, 6872, 9991), (1, 3436, 4995), (1, 1718, 2497)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (8342, 21340), (4171, 10670), (2085, 5335), (1042, 2667), (521, 1333)
│ └── 'nucleus_labels': DataTree[yx] (8309, 21321), (4154, 10660), (2077, 5330), (1038, 2665), (519, 1332)
├── Points
│ └── 'transcripts': DataFrame with shape: (1426272, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (10532, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (10532, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (10562, 2) (2D shapes)
└── Tables
└── 'table': AnnData (10532, 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("ixeRpknioc89ec9r0000")
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("ixeRpknioc89ec9r") # 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 ixeRpknioc89ec9r0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ixeRpknioc89ec9r
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ixeRpknioc89ec9rLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- glioma
- Modality
- RNA
- Observations (cells)
- 10,532
- Transcripts
- 1,426,272
- Tier
- bronze
- Size
- 1.8 GB
- Sample ID
- GSM9105221
- License
- NCBI GEO policy
- Published
- Sep 1, 2025
Cite this dataset
doi.org/10.1016/j.immuni.2025.09.018 ↗ BibTeX
@article{geo:GSM9105221,
doi = {10.1016/j.immuni.2025.09.018},
title = {GSM9105221},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB