10x Xenium
Mouse bone element
GSM9703599
silver Interactive viewer melanoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 27277, 42729), (1, 13638, 21364), (1, 6819, 10682), (1, 3409, 5341), (1, 1704, 2670)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (26582, 40977), (13291, 20488), (6645, 10244), (3322, 5122), (1661, 2561)
│ └── 'nucleus_labels': DataTree[yx] (26536, 40931), (13268, 20465), (6634, 10232), (3317, 5116), (1658, 2558)
├── Points
│ └── 'transcripts': DataFrame with shape: (5235879, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (77166, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (77166, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (78605, 2) (2D shapes)
└── Tables
└── 'table': AnnData (77166, 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("toR6hbN5PBWwRZeU0000")
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("toR6hbN5PBWwRZeU") # 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 toR6hbN5PBWwRZeU0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/toR6hbN5PBWwRZeU
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid toR6hbN5PBWwRZeULicense: 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
- Condition
- melanoma
- Modality
- RNA
- Observations (cells)
- 77,166
- Transcripts
- 5,235,879
- Tier
- silver
- Size
- 950 MB
- Sample ID
- GSM9703599
- 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