Visium
Human lymph node
human-lymph-node-1-standard-1-0-0
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'V1_Human_Lymph_Node_full_image': DataTree[cyx] (3, 11757, 11291), (3, 5878, 5645), (3, 2939, 2822), (3, 1469, 1411), (3, 734, 705)
│ ├── 'V1_Human_Lymph_Node_hires_image': DataArray[cyx] (3, 2000, 1921)
│ └── 'V1_Human_Lymph_Node_lowres_image': DataArray[cyx] (3, 600, 576)
├── Shapes
│ └── 'V1_Human_Lymph_Node': GeoDataFrame shape: (4039, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4039, 33538)
with coordinate systems:
▸ 'V1_Human_Lymph_Node', with elements:
V1_Human_Lymph_Node_full_image (Images), V1_Human_Lymph_Node_hires_image (Images), V1_Human_Lymph_Node_lowres_image (Images), V1_Human_Lymph_Node (Shapes)
▸ 'V1_Human_Lymph_Node_downscaled_hires', with elements:
V1_Human_Lymph_Node_hires_image (Images), V1_Human_Lymph_Node (Shapes)
▸ 'V1_Human_Lymph_Node_downscaled_lowres', with elements:
V1_Human_Lymph_Node_lowres_image (Images), V1_Human_Lymph_Node (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("NhmgFl1rhfk0bBAz0000")
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("NhmgFl1rhfk0bBAz") # 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 NhmgFl1rhfk0bBAz0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/NhmgFl1rhfk0bBAz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid NhmgFl1rhfk0bBAzLicense: CC BY 4.0
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lymph node
- Modality
- RNA
- Observations (spots)
- 4,039
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 11,291 × 11,757 px
- mpp
- 0.615 µm/px
- Size
- 352 MB
- Sample ID
- human-lymph-node-1-standard-1-0-0
- License
- CC BY 4.0
- Published
- Dec 12, 2019
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