10x Xenium
Human brain
GSM9461744
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20624, 25705), (1, 10312, 12852), (1, 5156, 6426), (1, 2578, 3213), (1, 1289, 1606)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20533, 25500), (10266, 12750), (5133, 6375), (2566, 3187), (1283, 1593)
│ └── 'nucleus_labels': DataTree[yx] (20511, 25466), (10255, 12733), (5127, 6366), (2563, 3183), (1281, 1591)
├── Points
│ └── 'transcripts': DataFrame with shape: (1303609, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (53044, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (53044, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (53067, 2) (2D shapes)
└── Tables
└── 'table': AnnData (53044, 5001)
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("9pP13jlQC4vfcENg0000")
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("9pP13jlQC4vfcENg") # 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 9pP13jlQC4vfcENg0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/9pP13jlQC4vfcENg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 9pP13jlQC4vfcENgLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 53,044
- Transcripts
- 1,303,609
- Tier
- bronze
- Size
- 901 MB
- Sample ID
- GSM9461744
- License
- NCBI GEO policy
- Published
- Mar 9, 2026
Cite this dataset
doi.org/10.1038/s41467-026-71803-3 ↗ BibTeX
@article{geo:GSM9461744,
doi = {10.1038/s41467-026-71803-3},
title = {GSM9461744},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB