Visium
Human breast
human-breast-cancer-block-a-section-1-1-standard-1-1-0
silver Interactive viewer H&E Invasive Ductal Carcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'V1_Breast_Cancer_Block_A_Section_1_full_image': DataTree[cyx] (3, 24240, 24240), (3, 12120, 12120), (3, 6060, 6060), (3, 3030, 3030), (3, 1515, 1515)
│ ├── 'V1_Breast_Cancer_Block_A_Section_1_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'V1_Breast_Cancer_Block_A_Section_1_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'V1_Breast_Cancer_Block_A_Section_1': GeoDataFrame shape: (3798, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3798, 36601)
with coordinate systems:
▸ 'V1_Breast_Cancer_Block_A_Section_1', with elements:
V1_Breast_Cancer_Block_A_Section_1_full_image (Images), V1_Breast_Cancer_Block_A_Section_1_hires_image (Images), V1_Breast_Cancer_Block_A_Section_1_lowres_image (Images), V1_Breast_Cancer_Block_A_Section_1 (Shapes)
▸ 'V1_Breast_Cancer_Block_A_Section_1_downscaled_hires', with elements:
V1_Breast_Cancer_Block_A_Section_1_hires_image (Images), V1_Breast_Cancer_Block_A_Section_1 (Shapes)
▸ 'V1_Breast_Cancer_Block_A_Section_1_downscaled_lowres', with elements:
V1_Breast_Cancer_Block_A_Section_1_lowres_image (Images), V1_Breast_Cancer_Block_A_Section_1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("UAmBmYBQdrTR5Sz20000")
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("UAmBmYBQdrTR5Sz2") # 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 UAmBmYBQdrTR5Sz20000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/UAmBmYBQdrTR5Sz2
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid UAmBmYBQdrTR5Sz2License: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- breast
- Condition
- Invasive Ductal Carcinoma
- Modality
- RNA
- Observations (spots)
- 3,798
- Tier
- silver
- Chemistry
- Visium v1
- Magnification
- 20x
- Resolution
- 24,240 × 24,240 px
- mpp
- 0.310 µm/px
- Size
- 1.6 GB
- Sample ID
- human-breast-cancer-block-a-section-1-1-standard-1-1-0
- License
- CC BY 4.0
- Published
- Jun 23, 2020
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