10x Xenium
Human nucleus accumbens
GSM9604822
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 108777, 51208), (1, 54388, 25604), (1, 27194, 12802), (1, 13597, 6401), (1, 6798, 3200)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (108389, 49280), (54194, 24640), (27097, 12320), (13548, 6160), (6774, 3080)
│ └── 'nucleus_labels': DataTree[yx] (108343, 49234), (54171, 24617), (27085, 12308), (13542, 6154), (6771, 3077)
├── Points
│ └── 'transcripts': DataFrame with shape: (117961875, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (228127, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (228127, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (228127, 2) (2D shapes)
└── Tables
└── 'table': AnnData (228127, 366)
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("jgjmrsPH60wrq9SV0000")
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("jgjmrsPH60wrq9SV") # 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 jgjmrsPH60wrq9SV0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/jgjmrsPH60wrq9SV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid jgjmrsPH60wrq9SVLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- nucleus accumbens
- Modality
- RNA
- Observations (cells)
- 228,127
- Transcripts
- 117,961,875
- Tier
- bronze
- Size
- 9.3 GB
- Sample ID
- GSM9604822
- License
- NCBI GEO policy
- Published
- Mar 30, 2026
Cite this dataset
doi.org/10.1016/j.neuron.2026.06.002 ↗ BibTeX
@article{geo:GSM9604822,
doi = {10.1016/j.neuron.2026.06.002},
title = {GSM9604822},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB