10x Xenium
Mouse skin of body
GSM8551250
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 98506, 39854), (1, 49253, 19927), (1, 24626, 9963), (1, 12313, 4981), (1, 6156, 2490)
├── Points
│ └── 'transcripts': DataFrame with shape: (34541873, 10) (3D points)
├── Shapes
│ └── 'cell_circles': GeoDataFrame shape: (332833, 2) (2D shapes)
└── Tables
└── 'table': AnnData (332833, 479)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), transcripts (Points), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("qDDM9NdqTCkLc5ys0000")
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("qDDM9NdqTCkLc5ys") # 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 qDDM9NdqTCkLc5ys0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/qDDM9NdqTCkLc5ys
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid qDDM9NdqTCkLc5ysLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- skin of body
- Modality
- RNA
- Observations (cells)
- 332,833
- Transcripts
- 34,541,873
- Tier
- bronze
- Size
- 5.2 GB
- Sample ID
- GSM8551250
- License
- NCBI GEO policy
- Published
- Oct 7, 2024
Cite this dataset
doi.org/10.1038/s43587-024-00755-4 ↗ BibTeX
@article{geo:GSM8551250,
doi = {10.1038/s43587-024-00755-4},
title = {GSM8551250},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB