10x Xenium
Human pancreas
ffpe-human-pancreas-with-xenium-multimodal-cell-segmentation-1-standard
silver Interactive viewer H&E pancreatic cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 27502, 14896), (3, 13751, 7448), (3, 6875, 3724), (3, 3437, 1862), (3, 1718, 931)
│ └── 'morphology_focus': DataTree[cyx] (4, 13770, 34155), (4, 6885, 17077), (4, 3442, 8538), (4, 1721, 4269), (4, 860, 2134)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13770, 34155), (6885, 17077), (3442, 8538), (1721, 4269), (860, 2134)
│ └── 'nucleus_labels': DataTree[yx] (13770, 34155), (6885, 17077), (3442, 8538), (1721, 4269), (860, 2134)
├── Points
│ └── 'transcripts': DataFrame with shape: (8073840, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (140702, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (140702, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (141810, 2) (2D shapes)
└── Tables
└── 'table': AnnData (140702, 377)
with coordinate systems:
▸ 'global', with elements:
he_image (Images), morphology_focus (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("IlEA4ms6c9S1OvBg") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/IlEA4ms6c9S1OvBg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid IlEA4ms6c9S1OvBg Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["IlEA4ms6c9S1OvBg0005"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
10x-ffpe-human-pancreas-with-xenium-multimodal-cell-segmentation→ 1 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- pancreas
- Condition
- pancreatic cancer
- Modality
- RNA
- Observations
- 140,702
- Transcripts
- 8,073,840
- Tier
- silver
- Chemistry
- Xenium v1
- Magnification
- 40x
- Resolution
- 14,896 × 27,502 px
- mpp
- 0.003 µm/px
- Size
- 4.3 GB
- Sample ID
- ffpe-human-pancreas-with-xenium-multimodal-cell-segmentation-1-standard
- License
- CC BY 4.0
- Published
- Mar 19, 2024
Cite this dataset
No linked publication found — please cite the data source: 10x Genomics ↗.
Source: 10x Genomics ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB