10x Xenium
Mouse bone element
GSM9703604
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27234, 48355), (1, 13617, 24177), (1, 6808, 12088), (1, 3404, 6044), (1, 1702, 3022)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (26031, 45605), (13015, 22802), (6507, 11401), (3253, 5700), (1626, 2850)
│ └── 'nucleus_labels': DataTree[yx] (25985, 45580), (12992, 22790), (6496, 11395), (3248, 5697), (1624, 2848)
├── Points
│ └── 'transcripts': DataFrame with shape: (9120943, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (169216, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (169216, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (171469, 2) (2D shapes)
└── Tables
└── 'table': AnnData (169216, 5046)
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("7SDnWe5k8scDxMHV0000")
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("7SDnWe5k8scDxMHV") # 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 7SDnWe5k8scDxMHV0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/7SDnWe5k8scDxMHV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7SDnWe5k8scDxMHVLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics of bone taken from two PRF1-/- B16F10-injected and one PRF1-/- healthy control- bone tissues using Xenium→ 6 datasets · comparison
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- bone element
- Modality
- RNA
- Observations (cells)
- 169,216
- Transcripts
- 9,120,943
- Tier
- silver
- Size
- 1.5 GB
- Sample ID
- GSM9703604
- License
- NCBI GEO policy
- Published
- Jul 28, 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