Visium HD
Human breast
visium-hd-cytassist-gene-expression-human-breast-cancer-fixed-frozen
silver Interactive viewer H&E breast cancer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'Visium_HD_Human_Breast_Cancer_Fixed_Frozen_full_image': DataTree[cyx] (3, 38345, 42052), (3, 19172, 21026), (3, 9586, 10513), (3, 4793, 5256), (3, 2396, 2628)
├── Shapes
│ ├── 'Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_002um': GeoDataFrame shape: (11187510, 1) (2D shapes)
│ ├── 'Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_008um': GeoDataFrame shape: (700193, 1) (2D shapes)
│ ├── 'Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_016um': GeoDataFrame shape: (175095, 1) (2D shapes)
│ └── 'Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_016um_for_vitessce': GeoDataFrame shape: (175095, 2) (2D shapes)
└── Tables
├── 'square_002um': AnnData (11187510, 18085)
├── 'square_008um': AnnData (700193, 18085)
└── 'square_016um': AnnData (175095, 18085)
with coordinate systems:
▸ 'Visium_HD_Human_Breast_Cancer_Fixed_Frozen', with elements:
Visium_HD_Human_Breast_Cancer_Fixed_Frozen_full_image (Images), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_002um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_008um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_016um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_Human_Breast_Cancer_Fixed_Frozen_downscaled_hires', with elements:
Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_002um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_008um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_016um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_Human_Breast_Cancer_Fixed_Frozen_downscaled_lowres', with elements:
Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_002um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_008um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_016um (Shapes), Visium_HD_Human_Breast_Cancer_Fixed_Frozen_square_016um_for_vitessce (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("uJNPd7W8tg5eOmao") # 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/uJNPd7W8tg5eOmao
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid uJNPd7W8tg5eOmao Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["uJNPd7W8tg5eOmao0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium HD
- Organism
- human
- Tissue
- breast
- Condition
- breast cancer
- Modality
- RNA
- Observations
- 700,193
- Tier
- silver
- Chemistry
- Visium HD v1
- Magnification
- 40x
- Resolution
- 42,052 × 38,345 px
- mpp
- 0.274 µm/px
- Size
- 7.0 GB
- Sample ID
- visium-hd-cytassist-gene-expression-human-breast-cancer-fixed-frozen
- License
- CC BY 4.0
- Published
- Sep 17, 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