10x Xenium
Human skin of body
human-skin-data-xenium-human-multi-tissue-and-cancer-panel-1-standard__hskin-nondiseased-section-1-ffpe
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 45276, 32390), (3, 22638, 16195), (3, 11319, 8097), (3, 5659, 4048), (3, 2829, 2024)
│ ├── 'morphology_focus': DataTree[cyx] (1, 44244, 53932), (1, 22122, 26966), (1, 11061, 13483), (1, 5530, 6741), (1, 2765, 3370)
│ └── 'morphology_mip': DataTree[cyx] (1, 44244, 53932), (1, 22122, 26966), (1, 11061, 13483), (1, 5530, 6741), (1, 2765, 3370)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (44244, 53932), (22122, 26966), (11061, 13483), (5530, 6741), (2765, 3370)
│ └── 'nucleus_labels': DataTree[yx] (44244, 53932), (22122, 26966), (11061, 13483), (5530, 6741), (2765, 3370)
├── Points
│ └── 'transcripts': DataFrame with shape: (2586609, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (68476, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (68476, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (68476, 1) (2D shapes)
└── Tables
└── 'table': AnnData (68476, 377)
with coordinate systems:
▸ 'global', with elements:
he_image (Images), 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("yY3XV9HxnHqU3ZC3") # 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/yY3XV9HxnHqU3ZC3
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yY3XV9HxnHqU3ZC3 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["yY3XV9HxnHqU3ZC30001"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
10x-human-skin-data-xenium-human-multi-tissue-and-cancer-panel-1-standard→ 2 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- skin of body
- Modality
- RNA
- Observations
- 68,476
- Transcripts
- 2,586,609
- Tier
- silver
- Chemistry
- Xenium v1
- Magnification
- 40x
- Resolution
- 32,390 × 45,276 px
- mpp
- 0.001 µm/px
- Size
- 7.2 GB
- Sample ID
- human-skin-data-xenium-human-multi-tissue-and-cancer-panel-1-standard__hskin-nondiseased-section-1-ffpe
- License
- CC BY 4.0
- Published
- Mar 5, 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