Visium
Human spinal cord
human-spinal-cord-whole-transcriptome-analysis-stains-dapi-anti-snap-25-anti-gfap-anti-myelin-cn-pase-1-standard-1-2-0
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'Parent_Visium_Human_SpinalCord_full_image': DataTree[cyx] (4, 4444, 4444), (4, 2222, 2222), (4, 1111, 1111), (4, 555, 555), (4, 277, 277)
│ ├── 'Parent_Visium_Human_SpinalCord_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'Parent_Visium_Human_SpinalCord_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'Parent_Visium_Human_SpinalCord': GeoDataFrame shape: (2812, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2812, 36601)
with coordinate systems:
▸ 'Parent_Visium_Human_SpinalCord', with elements:
Parent_Visium_Human_SpinalCord_full_image (Images), Parent_Visium_Human_SpinalCord_hires_image (Images), Parent_Visium_Human_SpinalCord_lowres_image (Images), Parent_Visium_Human_SpinalCord (Shapes)
▸ 'Parent_Visium_Human_SpinalCord_downscaled_hires', with elements:
Parent_Visium_Human_SpinalCord_hires_image (Images), Parent_Visium_Human_SpinalCord (Shapes)
▸ 'Parent_Visium_Human_SpinalCord_downscaled_lowres', with elements:
Parent_Visium_Human_SpinalCord_lowres_image (Images), Parent_Visium_Human_SpinalCord (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Z0ok19LvFG4ahQln") # 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/Z0ok19LvFG4ahQln
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Z0ok19LvFG4ahQln Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Z0ok19LvFG4ahQln0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- Visium
- Organism
- human
- Tissue
- spinal cord
- Modality
- RNA
- Observations
- 2,812
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 2,000 px
- mpp
- 4.095 µm/px
- Size
- 153 MB
- Sample ID
- human-spinal-cord-whole-transcriptome-analysis-stains-dapi-anti-snap-25-anti-gfap-anti-myelin-cn-pase-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