10x Xenium
Mouse bone element
GSM9703603
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37414, 37089), (1, 18707, 18544), (1, 9353, 9272), (1, 4676, 4636), (1, 2338, 2318)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (36017, 34416), (18008, 17208), (9004, 8604), (4502, 4302), (2251, 2151)
│ └── 'nucleus_labels': DataTree[yx] (35994, 34409), (17997, 17204), (8998, 8602), (4499, 4301), (2249, 2150)
├── Points
│ └── 'transcripts': DataFrame with shape: (9476342, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (182887, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (182887, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (187879, 2) (2D shapes)
└── Tables
└── 'table': AnnData (182887, 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("5czGjO9HtuHADXH50000")
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("5czGjO9HtuHADXH5") # 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 5czGjO9HtuHADXH50000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5czGjO9HtuHADXH5
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5czGjO9HtuHADXH5License: 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)
- 182,887
- Transcripts
- 9,476,342
- Tier
- silver
- Size
- 1.5 GB
- Sample ID
- GSM9703603
- 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