10x Xenium
Human brain
GSM9105216
bronze Interactive viewer glioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27474, 39928), (1, 13737, 19964), (1, 6868, 9982), (1, 3434, 4991), (1, 1717, 2495)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (10285, 37525), (5142, 18762), (2571, 9381), (1285, 4690), (642, 2345)
│ └── 'nucleus_labels': DataTree[yx] (10272, 37515), (5136, 18757), (2568, 9378), (1284, 4689), (642, 2344)
├── Points
│ └── 'transcripts': DataFrame with shape: (2062213, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (12085, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (12085, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (12317, 2) (2D shapes)
└── Tables
└── 'table': AnnData (12085, 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("X0wU2nvV4w1OeoPl0000")
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("X0wU2nvV4w1OeoPl") # 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 X0wU2nvV4w1OeoPl0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/X0wU2nvV4w1OeoPl
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid X0wU2nvV4w1OeoPlLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- glioma
- Modality
- RNA
- Observations (cells)
- 12,085
- Transcripts
- 2,062,213
- Tier
- bronze
- Size
- 1.6 GB
- Sample ID
- GSM9105216
- License
- NCBI GEO policy
- Published
- Sep 1, 2025
Cite this dataset
doi.org/10.1016/j.immuni.2025.09.018 ↗ BibTeX
@article{geo:GSM9105216,
doi = {10.1016/j.immuni.2025.09.018},
title = {GSM9105216},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB