Visium
Mouse lung
CellRanger analyzed Visium data (WT_Visium)
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'WT_Visium_hires_image': DataArray[cyx] (3, 2000, 1973)
│ └── 'WT_Visium_lowres_image': DataArray[cyx] (3, 600, 592)
├── Shapes
│ └── 'WT_Visium': GeoDataFrame shape: (3601, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3601, 19465)
with coordinate systems:
▸ 'WT_Visium', with elements:
WT_Visium_hires_image (Images), WT_Visium_lowres_image (Images), WT_Visium (Shapes)
▸ 'WT_Visium_downscaled_hires', with elements:
WT_Visium_hires_image (Images), WT_Visium (Shapes)
▸ 'WT_Visium_downscaled_lowres', with elements:
WT_Visium_lowres_image (Images), WT_Visium (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("Jp6pD4m0JRbbZ3R20000")
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("Jp6pD4m0JRbbZ3R2") # 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 Jp6pD4m0JRbbZ3R20000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Jp6pD4m0JRbbZ3R2
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Jp6pD4m0JRbbZ3R2License: CC BY 4.0
Metadata
- Technology
- Visium
- Vendor
- 10x Genomics
- Organism
- mouse
- Tissue
- lung
- Modality
- RNA
- Observations (spots)
- 3,601
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,973 × 2,000 px
- mpp
- 3.388 µm/px
- Size
- 56.2 MB
- Sample ID
- 25584672:WT_Visium
- License
- CC BY 4.0
- Published
- Aug 2, 2024
Cite this dataset
doi.org/10.6084/m9.figshare.25584672.v1 ↗ BibTeX
@article{figshare:25584672,
doi = {10.6084/m9.figshare.25584672.v1},
title = {CellRanger analyzed Visium data (TKO_Visium)},
year = {2024}
}Source: figshare.com ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB