10x Xenium
Human brain
GSM9105220
bronze Interactive viewer glioma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 23939, 28545), (1, 11969, 14272), (1, 5984, 7136), (1, 2992, 3568), (1, 1496, 1784)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13686, 13170), (6843, 6585), (3421, 3292), (1710, 1646), (855, 823)
│ └── 'nucleus_labels': DataTree[yx] (13680, 13154), (6840, 6577), (3420, 3288), (1710, 1644), (855, 822)
├── Points
│ └── 'transcripts': DataFrame with shape: (782454, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (4394, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (4394, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (4539, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4394, 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("W1AcW7hqyze672Fg0000")
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("W1AcW7hqyze672Fg") # 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 W1AcW7hqyze672Fg0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/W1AcW7hqyze672Fg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid W1AcW7hqyze672FgLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Condition
- glioma
- Modality
- RNA
- Observations (cells)
- 4,394
- Transcripts
- 782,454
- Tier
- bronze
- Size
- 836 MB
- Sample ID
- GSM9105220
- License
- NCBI GEO policy
- Published
- Sep 1, 2025
Cite this dataset
doi.org/10.1016/j.immuni.2025.09.018 ↗ BibTeX
@article{geo:GSM9105220,
doi = {10.1016/j.immuni.2025.09.018},
title = {GSM9105220},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB