10x Xenium
Human brain
GSM9105222
bronze Interactive viewer glioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 47894, 48385), (1, 23947, 24192), (1, 11973, 12096), (1, 5986, 6048), (1, 2993, 3024)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (14948, 12949), (7474, 6474), (3737, 3237), (1868, 1618), (934, 809)
│ └── 'nucleus_labels': DataTree[yx] (14939, 12930), (7469, 6465), (3734, 3232), (1867, 1616), (933, 808)
├── Points
│ └── 'transcripts': DataFrame with shape: (507561, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (3532, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (3532, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (3590, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3532, 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("pMHmvdHIO3nl04R00000")
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("pMHmvdHIO3nl04R0") # 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 pMHmvdHIO3nl04R00000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pMHmvdHIO3nl04R0
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pMHmvdHIO3nl04R0License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- glioma
- Modality
- RNA
- Observations (cells)
- 3,532
- Transcripts
- 507,561
- Tier
- bronze
- Size
- 2.9 GB
- Sample ID
- GSM9105222
- License
- NCBI GEO policy
- Published
- Sep 1, 2025
Cite this dataset
doi.org/10.1016/j.immuni.2025.09.018 ↗ BibTeX
@article{geo:GSM9105222,
doi = {10.1016/j.immuni.2025.09.018},
title = {GSM9105222},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB