10x Xenium
Human lymph node
GSM8193671
bronze Interactive viewer head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 37530, 34153), (1, 18765, 17076), (1, 9382, 8538), (1, 4691, 4269), (1, 2345, 2134)
├── Points
│ └── 'transcripts': DataFrame with shape: (75683914, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (309309, 2) (2D shapes)
└── Tables
└── 'table': AnnData (309309, 377)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("eGZ5oUW5xyRtB2Ln0000")
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("eGZ5oUW5xyRtB2Ln") # 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 eGZ5oUW5xyRtB2Ln0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/eGZ5oUW5xyRtB2Ln
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid eGZ5oUW5xyRtB2LnLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lymph node
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations (cells)
- 309,309
- Transcripts
- 75,683,914
- Tier
- bronze
- Size
- 5.0 GB
- Sample ID
- GSM8193671
- License
- NCBI GEO policy
- Published
- Jun 23, 2024
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