10x Xenium
Crab-eating macaque mediastinal lymph node
GSM10039418
silver Interactive viewer COVID-19 No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 101947, 51109), (1, 50973, 25554), (1, 25486, 12777), (1, 12743, 6388), (1, 6371, 3194)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (101504, 50313), (50752, 25156), (25376, 12578), (12688, 6289), (6344, 3144)
│ └── 'nucleus_labels': DataTree[yx] (101364, 50173), (50682, 25086), (25341, 12543), (12670, 6271), (6335, 3135)
├── Points
│ └── 'transcripts': DataFrame with shape: (82682722, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (1859898, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (1859898, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (1859898, 1) (2D shapes)
└── Tables
└── 'table': AnnData (1859898, 377)
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("JgRGzGs9Itx1vdh20000")
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("JgRGzGs9Itx1vdh2") # 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 JgRGzGs9Itx1vdh20000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/JgRGzGs9Itx1vdh2
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid JgRGzGs9Itx1vdh2License: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- crab-eating macaque
- Tissue
- mediastinal lymph node
- Condition
- COVID-19
- Modality
- RNA
- Observations (cells)
- 1,859,898
- Transcripts
- 82,682,722
- Tier
- silver
- Size
- 8.7 GB
- Sample ID
- GSM10039418
- License
- NCBI GEO policy
- Published
- Sep 13, 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