10x Xenium
Mouse colon
fresh-frozen-mouse-colon-with-xenium-multimodal-cell-segmentation-1-standard
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 28329, 32201), (3, 14164, 16100), (3, 7082, 8050), (3, 3541, 4025), (3, 1770, 2012)
│ └── 'morphology_focus': DataTree[cyx] (4, 34104, 28482), (4, 17052, 14241), (4, 8526, 7120), (4, 4263, 3560), (4, 2131, 1780)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (34104, 28482), (17052, 14241), (8526, 7120), (4263, 3560), (2131, 1780)
│ └── 'nucleus_labels': DataTree[yx] (34104, 28482), (17052, 14241), (8526, 7120), (4263, 3560), (2131, 1780)
├── Points
│ └── 'transcripts': DataFrame with shape: (82549008, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (219797, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (219797, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (218741, 2) (2D shapes)
└── Tables
└── 'table': AnnData (219797, 379)
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("xTLyS1AdjfKzI25v") # 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/xTLyS1AdjfKzI25v
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xTLyS1AdjfKzI25v Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["xTLyS1AdjfKzI25v0001"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
10x-fresh-frozen-mouse-colon-xenium-multimodal-cell-segmentation→ 1 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- colon
- Modality
- RNA
- Observations
- 219,797
- Transcripts
- 82,549,008
- Tier
- silver
- Chemistry
- Xenium v1
- Magnification
- 40x
- Resolution
- 32,201 × 28,329 px
- mpp
- 0.005 µm/px
- Size
- 9.5 GB
- Sample ID
- fresh-frozen-mouse-colon-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