Visium
Human breast
human-breast-cancer-visium-fresh-frozen-whole-transcriptome-1-standard
silver Interactive viewer H&E breast cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Visium_Human_Breast_Cancer_full_image': DataTree[cyx] (3, 27755, 41572), (3, 13877, 20786), (3, 6938, 10393), (3, 3469, 5196), (3, 1734, 2598)
│ ├── 'Visium_Human_Breast_Cancer_hires_image': DataArray[cyx] (3, 1335, 2000)
│ └── 'Visium_Human_Breast_Cancer_lowres_image': DataArray[cyx] (3, 401, 600)
├── Shapes
│ └── 'Visium_Human_Breast_Cancer': GeoDataFrame shape: (4898, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4898, 36601)
with coordinate systems:
▸ 'Visium_Human_Breast_Cancer', with elements:
Visium_Human_Breast_Cancer_full_image (Images), Visium_Human_Breast_Cancer_hires_image (Images), Visium_Human_Breast_Cancer_lowres_image (Images), Visium_Human_Breast_Cancer (Shapes)
▸ 'Visium_Human_Breast_Cancer_downscaled_hires', with elements:
Visium_Human_Breast_Cancer_hires_image (Images), Visium_Human_Breast_Cancer (Shapes)
▸ 'Visium_Human_Breast_Cancer_downscaled_lowres', with elements:
Visium_Human_Breast_Cancer_lowres_image (Images), Visium_Human_Breast_Cancer (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("mJw05GsY9H7iDM2J0000")
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("mJw05GsY9H7iDM2J") # 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 mJw05GsY9H7iDM2J0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/mJw05GsY9H7iDM2J
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid mJw05GsY9H7iDM2JLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations (spots)
- 4,898
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 41,572 × 27,755 px
- mpp
- 0.312 µm/px
- Size
- 2.5 GB
- Sample ID
- human-breast-cancer-visium-fresh-frozen-whole-transcriptome-1-standard
- License
- CC BY 4.0
- Published
- Jul 1, 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