10x Xenium
Mouse pancreas
GSM9921339
silver Interactive viewer pancreatic ductal adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 34103, 48349), (1, 17051, 24174), (1, 8525, 12087), (1, 4262, 6043), (1, 2131, 3021)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (32393, 48044), (16196, 24022), (8098, 12011), (4049, 6005), (2024, 3002)
│ └── 'nucleus_labels': DataTree[yx] (32346, 46824), (16173, 23412), (8086, 11706), (4043, 5853), (2021, 2926)
├── Points
│ └── 'transcripts': DataFrame with shape: (60135669, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (386542, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (386542, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (387927, 2) (2D shapes)
└── Tables
└── 'table': AnnData (386542, 475)
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("JRVypxhX31FhreFn0000")
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("JRVypxhX31FhreFn") # 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 JRVypxhX31FhreFn0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/JRVypxhX31FhreFn
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid JRVypxhX31FhreFnLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- pancreas
- Condition
- pancreatic ductal adenocarcinoma
- Modality
- RNA
- Observations (cells)
- 386,542
- Transcripts
- 60,135,669
- Tier
- silver
- Size
- 3.6 GB
- Sample ID
- GSM9921339
- License
- NCBI GEO policy
- Published
- Aug 27, 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