Visium
Human large intestine
human-colorectal-cancer-targeted-gene-signature-panel-1-standard-1-2-0
silver Interactive viewer H&E colorectal adenocarcinoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Targeted_Visium_Human_ColorectalCancer_GeneSignature_full_image': DataTree[cyx] (3, 13332, 13332), (3, 6666, 6666), (3, 3333, 3333), (3, 1666, 1666), (3, 833, 833)
│ ├── 'Targeted_Visium_Human_ColorectalCancer_GeneSignature_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'Targeted_Visium_Human_ColorectalCancer_GeneSignature_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'Targeted_Visium_Human_ColorectalCancer_GeneSignature': GeoDataFrame shape: (3138, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3138, 1142)
with coordinate systems:
▸ 'Targeted_Visium_Human_ColorectalCancer_GeneSignature', with elements:
Targeted_Visium_Human_ColorectalCancer_GeneSignature_full_image (Images), Targeted_Visium_Human_ColorectalCancer_GeneSignature_hires_image (Images), Targeted_Visium_Human_ColorectalCancer_GeneSignature_lowres_image (Images), Targeted_Visium_Human_ColorectalCancer_GeneSignature (Shapes)
▸ 'Targeted_Visium_Human_ColorectalCancer_GeneSignature_downscaled_hires', with elements:
Targeted_Visium_Human_ColorectalCancer_GeneSignature_hires_image (Images), Targeted_Visium_Human_ColorectalCancer_GeneSignature (Shapes)
▸ 'Targeted_Visium_Human_ColorectalCancer_GeneSignature_downscaled_lowres', with elements:
Targeted_Visium_Human_ColorectalCancer_GeneSignature_lowres_image (Images), Targeted_Visium_Human_ColorectalCancer_GeneSignature (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("djB7Xa8QBdndXWbt") # 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/djB7Xa8QBdndXWbt
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid djB7Xa8QBdndXWbt Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["djB7Xa8QBdndXWbt0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- large intestine
- Condition
- colorectal adenocarcinoma
- Modality
- RNA
- Observations
- 3,138
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 13,332 × 13,332 px
- mpp
- 0.614 µm/px
- Size
- 351 MB
- Sample ID
- human-colorectal-cancer-targeted-gene-signature-panel-1-standard-1-2-0
- License
- CC BY 4.0
- Published
- Oct 27, 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