Visium
Human skin of body
human-melanoma-if-stained-ffpe-2-standard
silver Interactive viewer H&E melanoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'CytAssist_FFPE_Human_Skin_Melanoma_full_image': DataTree[cyx] (4, 24536, 22098), (4, 12268, 11049), (4, 6134, 5524), (4, 3067, 2762), (4, 1533, 1381)
│ ├── 'CytAssist_FFPE_Human_Skin_Melanoma_hires_image': DataArray[cyx] (3, 2000, 1801)
│ └── 'CytAssist_FFPE_Human_Skin_Melanoma_lowres_image': DataArray[cyx] (3, 600, 541)
├── Shapes
│ └── 'CytAssist_FFPE_Human_Skin_Melanoma': GeoDataFrame shape: (3458, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3458, 18085)
with coordinate systems:
▸ 'CytAssist_FFPE_Human_Skin_Melanoma', with elements:
CytAssist_FFPE_Human_Skin_Melanoma_full_image (Images), CytAssist_FFPE_Human_Skin_Melanoma_hires_image (Images), CytAssist_FFPE_Human_Skin_Melanoma_lowres_image (Images), CytAssist_FFPE_Human_Skin_Melanoma (Shapes)
▸ 'CytAssist_FFPE_Human_Skin_Melanoma_downscaled_hires', with elements:
CytAssist_FFPE_Human_Skin_Melanoma_hires_image (Images), CytAssist_FFPE_Human_Skin_Melanoma (Shapes)
▸ 'CytAssist_FFPE_Human_Skin_Melanoma_downscaled_lowres', with elements:
CytAssist_FFPE_Human_Skin_Melanoma_lowres_image (Images), CytAssist_FFPE_Human_Skin_Melanoma (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("LqSr9Rjv3YT3FlvO") # 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/LqSr9Rjv3YT3FlvO
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid LqSr9Rjv3YT3FlvO Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["LqSr9Rjv3YT3FlvO0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- skin of body
- Condition
- melanoma
- Modality
- RNA
- Observations
- 3,458
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 1,801 × 2,000 px
- mpp
- 3.131 µm/px
- Size
- 4.0 GB
- Sample ID
- human-melanoma-if-stained-ffpe-2-standard
- License
- CC BY 4.0
- Published
- Jul 12, 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