10x Xenium
Human colon
human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard__hcolon-non-diseased-add-on-ffpe
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 30954, 45659), (1, 15477, 22829), (1, 7738, 11414), (1, 3869, 5707), (1, 1934, 2853)
│ └── 'morphology_mip': DataTree[cyx] (1, 30954, 45659), (1, 15477, 22829), (1, 7738, 11414), (1, 3869, 5707), (1, 1934, 2853)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30954, 45659), (15477, 22829), (7738, 11414), (3869, 5707), (1934, 2853)
│ └── 'nucleus_labels': DataTree[yx] (30954, 45659), (15477, 22829), (7738, 11414), (3869, 5707), (1934, 2853)
├── Points
│ └── 'transcripts': DataFrame with shape: (39573169, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (275822, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (275822, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (275822, 1) (2D shapes)
└── Tables
└── 'table': AnnData (275822, 425)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (Images), morphology_mip (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("1Fn1jXIrYRqetnxm") # 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/1Fn1jXIrYRqetnxm
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1Fn1jXIrYRqetnxm Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["1Fn1jXIrYRqetnxm0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- colon
- Modality
- RNA
- Observations
- 275,822
- Transcripts
- 39,573,169
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 4.9 GB
- Sample ID
- human-colon-preview-data-xenium-human-colon-gene-expression-panel-1-standard__hcolon-non-diseased-add-on-ffpe
- License
- CC BY 4.0
- Published
- Aug 29, 2023
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