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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("LqSr9Rjv3YT3FlvO0000")
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("LqSr9Rjv3YT3FlvO") # 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 LqSr9Rjv3YT3FlvO0000 --dest data/
# or lamin: 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 LqSr9Rjv3YT3FlvOLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- skin of body
- Condition
- melanoma
- Modality
- RNA
- Observations (spots)
- 3,458
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 1,801 × 2,000 px
- mpp
- 3.131 µm/px
- Size
- 4.3 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