10x Xenium
Human lung
preview-data-ffpe-human-lung-cancer-with-xenium-multimodal-cell-segmentation-1-standard
silver Interactive viewer H&E lung cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'he_image': DataTree[cyx] (3, 45087, 11580), (3, 22543, 5790), (3, 11271, 2895), (3, 5635, 1447), (3, 2817, 723)
│ └── 'morphology_focus': DataTree[cyx] (4, 17098, 51187), (4, 8549, 25593), (4, 4274, 12796), (4, 2137, 6398), (4, 1068, 3199)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17098, 51187), (8549, 25593), (4274, 12796), (2137, 6398), (1068, 3199)
│ └── 'nucleus_labels': DataTree[yx] (17098, 51187), (8549, 25593), (4274, 12796), (2137, 6398), (1068, 3199)
├── Points
│ └── 'transcripts': DataFrame with shape: (12165021, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (162254, 1) (2D shapes)
│ └── 'cell_circles': GeoDataFrame shape: (162254, 2) (2D shapes)
└── Tables
└── 'table': AnnData (162254, 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) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("tS2jpxnC9NS4FKBs") # 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/tS2jpxnC9NS4FKBs
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid tS2jpxnC9NS4FKBs Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["tS2jpxnC9NS4FKBs0001"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
10x-preview-ffpe-human-lung-cancer-xenium-multimodal-cell-segmentation→ 1 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- lung
- Condition
- lung cancer
- Modality
- RNA
- Observations
- 162,254
- Transcripts
- 12,165,021
- Tier
- silver
- Chemistry
- Xenium v1
- Magnification
- 40x
- Resolution
- 11,580 × 45,087 px
- mpp
- 0.005 µm/px
- Size
- 5.5 GB
- Sample ID
- preview-data-ffpe-human-lung-cancer-with-xenium-multimodal-cell-segmentation-1-standard
- License
- CC BY 4.0
- Published
- Feb 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