Visium HD
Human tonsil
visium-hd-cytassist-gene-expression-human-tonsil-fresh-frozen-if
silver Interactive viewer No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'Visium_HD_Human_Tonsil_Fresh_Frozen_IF_full_image': DataTree[cyx] (4, 25090, 26510), (4, 12545, 13255), (4, 6272, 6627), (4, 3136, 3313), (4, 1568, 1656)
├── Shapes
│ ├── 'Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_002um': GeoDataFrame shape: (10859964, 1) (2D shapes)
│ ├── 'Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_008um': GeoDataFrame shape: (679294, 1) (2D shapes)
│ ├── 'Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_016um': GeoDataFrame shape: (170034, 1) (2D shapes)
│ └── 'Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_016um_for_vitessce': GeoDataFrame shape: (170034, 2) (2D shapes)
└── Tables
├── 'square_002um': AnnData (10859964, 18085)
├── 'square_008um': AnnData (679294, 18085)
└── 'square_016um': AnnData (170034, 18085)
with coordinate systems:
▸ 'Visium_HD_Human_Tonsil_Fresh_Frozen_IF', with elements:
Visium_HD_Human_Tonsil_Fresh_Frozen_IF_full_image (Images), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_002um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_008um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_016um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_Human_Tonsil_Fresh_Frozen_IF_downscaled_hires', with elements:
Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_002um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_008um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_016um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_016um_for_vitessce (Shapes)
▸ 'Visium_HD_Human_Tonsil_Fresh_Frozen_IF_downscaled_lowres', with elements:
Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_002um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_008um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_016um (Shapes), Visium_HD_Human_Tonsil_Fresh_Frozen_IF_square_016um_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("QFYjcwtG1rjJJcsA0000")
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("QFYjcwtG1rjJJcsA") # 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 QFYjcwtG1rjJJcsA0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/QFYjcwtG1rjJJcsA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid QFYjcwtG1rjJJcsALicense: CC BY 4.0
Metadata
- Technology
- Visium HD
- Organism
- human
- Tissue
- tonsil
- Modality
- RNA
- Observations (bins)
- 679,294
- Tier
- silver
- Chemistry
- Visium HD v1
- Size
- 7.7 GB
- Sample ID
- visium-hd-cytassist-gene-expression-human-tonsil-fresh-frozen-if
- License
- CC BY 4.0
- Published
- Sep 17, 2024
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