10x Xenium
Mouse brain
GSM7871988
bronze Interactive viewer diffuse midline glioma, H3 K27M-mutant Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 20494, 28456), (1, 10247, 14228), (1, 5123, 7114), (1, 2561, 3557), (1, 1280, 1778)
├── Points
│ └── 'transcripts': DataFrame with shape: (39451251, 9) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (44941, 2) (2D shapes)
└── Tables
└── 'table': AnnData (44941, 298)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("Ss3e0BVDwS1YKqSn0000")
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("Ss3e0BVDwS1YKqSn") # 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 Ss3e0BVDwS1YKqSn0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Ss3e0BVDwS1YKqSn
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Ss3e0BVDwS1YKqSnLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Condition
- diffuse midline glioma, H3 K27M-mutant
- Modality
- RNA
- Observations (cells)
- 44,941
- Transcripts
- 13,150,417
- Tier
- bronze
- Size
- 1.0 GB
- Sample ID
- GSM7871988
- License
- NCBI GEO policy
- Published
- Nov 4, 2023
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