10x Xenium
Human lung
GSM9509139
bronze Interactive viewer squamous cell lung carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 23894, 25626), (4, 11947, 12813), (4, 5973, 6406), (4, 2986, 3203), (4, 1493, 1601)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (21489, 25310), (10744, 12655), (5372, 6327), (2686, 3163), (1343, 1581)
│ └── 'nucleus_labels': DataTree[yx] (19653, 25258), (9826, 12629), (4913, 6314), (2456, 3157), (1228, 1578)
├── Points
│ └── 'transcripts': DataFrame with shape: (15175810, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (78955, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (78955, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (79038, 2) (2D shapes)
└── Tables
└── 'table': AnnData (78955, 5001)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (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("ig5lXDmSfZCU5dVh0000")
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("ig5lXDmSfZCU5dVh") # 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 ig5lXDmSfZCU5dVh0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ig5lXDmSfZCU5dVh
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ig5lXDmSfZCU5dVhLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lung
- Condition
- squamous cell lung carcinoma
- Modality
- RNA
- Observations (cells)
- 78,955
- Transcripts
- 15,175,810
- Tier
- bronze
- Size
- 2.9 GB
- Sample ID
- GSM9509139
- License
- NCBI GEO policy
- Published
- Mar 27, 2026
Cite this dataset
doi.org/10.1038/s41592-026-03089-8 ↗ BibTeX
@article{geo:GSM9509139,
doi = {10.1038/s41592-026-03089-8},
title = {GSM9509139},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB