10x Xenium
Mouse brain
GSM9852124
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 30718, 45501), (1, 15359, 22750), (1, 7679, 11375), (1, 3839, 5687), (1, 1919, 2843)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30575, 44741), (15287, 22370), (7643, 11185), (3821, 5592), (1910, 2796)
│ └── 'nucleus_labels': DataTree[yx] (29749, 43424), (14874, 21712), (7437, 10856), (3718, 5428), (1859, 2714)
├── Points
│ └── 'transcripts': DataFrame with shape: (85451135, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (93056, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (93056, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (93564, 2) (2D shapes)
└── Tables
└── 'table': AnnData (93056, 347)
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("rrfmhldSzfhkk9I70000")
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("rrfmhldSzfhkk9I7") # 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 rrfmhldSzfhkk9I70000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/rrfmhldSzfhkk9I7
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid rrfmhldSzfhkk9I7License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (cells)
- 93,056
- Transcripts
- 85,451,135
- Tier
- silver
- Size
- 3.5 GB
- Sample ID
- GSM9852124
- License
- NCBI GEO policy
- Published
- Jul 30, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB