Visium
Human prostate gland
human-prostate-cancer-adenocarcinoma-with-invasive-carcinoma-ffpe-1-standard-1-3-0
silver Interactive viewer H&E prostate adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_FFPE_Human_Prostate_Cancer_full_image': DataTree[cyx] (3, 25219, 27482), (3, 12609, 13741), (3, 6304, 6870), (3, 3152, 3435), (3, 1576, 1717)
│ ├── 'Visium_FFPE_Human_Prostate_Cancer_hires_image': DataArray[cyx] (3, 1836, 2000)
│ └── 'Visium_FFPE_Human_Prostate_Cancer_lowres_image': DataArray[cyx] (3, 551, 600)
├── Shapes
│ └── 'Visium_FFPE_Human_Prostate_Cancer': GeoDataFrame shape: (4371, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4371, 17943)
with coordinate systems:
▸ 'Visium_FFPE_Human_Prostate_Cancer', with elements:
Visium_FFPE_Human_Prostate_Cancer_full_image (Images), Visium_FFPE_Human_Prostate_Cancer_hires_image (Images), Visium_FFPE_Human_Prostate_Cancer_lowres_image (Images), Visium_FFPE_Human_Prostate_Cancer (Shapes)
▸ 'Visium_FFPE_Human_Prostate_Cancer_downscaled_hires', with elements:
Visium_FFPE_Human_Prostate_Cancer_hires_image (Images), Visium_FFPE_Human_Prostate_Cancer (Shapes)
▸ 'Visium_FFPE_Human_Prostate_Cancer_downscaled_lowres', with elements:
Visium_FFPE_Human_Prostate_Cancer_lowres_image (Images), Visium_FFPE_Human_Prostate_Cancer (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("yp2ifz45Sxh6kiRt") # 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/yp2ifz45Sxh6kiRt
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yp2ifz45Sxh6kiRt Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["yp2ifz45Sxh6kiRt0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- prostate gland
- Condition
- prostate adenocarcinoma
- Modality
- RNA
- Observations
- 4,371
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 40x
- Resolution
- 27,482 × 25,219 px
- mpp
- 0.292 µm/px
- Size
- 1.9 GB
- Sample ID
- human-prostate-cancer-adenocarcinoma-with-invasive-carcinoma-ffpe-1-standard-1-3-0
- License
- CC BY 4.0
- Published
- Jun 9, 2021
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