10x Xenium

Human nucleus accumbens

GSM9604824

bronze Interactive viewer Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'morphology_mip': DataTree[cyx] (1, 81502, 54449), (1, 40751, 27224), (1, 20375, 13612), (1, 10187, 6806), (1, 5093, 3403)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (79488, 53793), (39744, 26896), (19872, 13448), (9936, 6724), (4968, 3362)
│     └── 'nucleus_labels': DataTree[yx] (79443, 53747), (39721, 26873), (19860, 13436), (9930, 6718), (4965, 3359)
├── Points
│     └── 'transcripts': DataFrame with shape: (23345111, 13) (3D points)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (188503, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (188503, 2) (2D shapes)
│     └── 'nucleus_boundaries': GeoDataFrame shape: (188503, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (188503, 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)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("6waJKpYX6H586cYX0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("6waJKpYX6H586cYX")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download 6waJKpYX6H586cYX0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/6waJKpYX6H586cYX

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 6waJKpYX6H586cYX

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Metadata

Technology: 10x Xenium
Organism: human
Tissue: nucleus accumbens
Modality: RNA
Observations (cells): 188,503
Transcripts: 23,345,111
Tier: bronze
Size: 6.3 GB
Sample ID: GSM9604824
License: NCBI GEO policy
Published: Mar 30, 2026

Cite this dataset

doi.org/10.1016/j.neuron.2026.06.002 ↗

BibTeX

@article{geo:GSM9604824,
  doi = {10.1016/j.neuron.2026.06.002},
  title = {GSM9604824},
  year = {2026}
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB