Visium
Human lung
human-lung-cancer-ffpe-2-standard
silver Interactive viewer H&E lung cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_full_image': DataTree[cyx] (3, 29395, 35637), (3, 14697, 17818), (3, 7348, 8909), (3, 3674, 4454), (3, 1837, 2227)
│ ├── 'CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_hires_image': DataArray[cyx] (3, 1650, 2000)
│ └── 'CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_lowres_image': DataArray[cyx] (3, 495, 600)
├── Shapes
│ └── 'CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma': GeoDataFrame shape: (3858, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3858, 18085)
with coordinate systems:
▸ 'CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma', with elements:
CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_full_image (Images), CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_hires_image (Images), CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_lowres_image (Images), CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma (Shapes)
▸ 'CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_downscaled_hires', with elements:
CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_hires_image (Images), CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma (Shapes)
▸ 'CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_downscaled_lowres', with elements:
CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma_lowres_image (Images), CytAssist_FFPE_Human_Lung_Squamous_Cell_Carcinoma (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("Wzknw691YzwJrG7m0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Wzknw691YzwJrG7m") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download Wzknw691YzwJrG7m0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Wzknw691YzwJrG7m
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Wzknw691YzwJrG7mLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lung
- Condition
- lung cancer
- Modality
- RNA
- Observations (spots)
- 3,858
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Magnification
- 40x
- Resolution
- 35,637 × 29,395 px
- mpp
- 0.215 µm/px
- Size
- 2.5 GB
- Sample ID
- human-lung-cancer-ffpe-2-standard
- License
- CC BY 4.0
- Published
- Jul 13, 2022
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