Visium
Human liver
GSM7968253
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7968253_NL15_hires_image': DataArray[cyx] (3, 2000, 1819)
│ └── 'GSM7968253_NL15_lowres_image': DataArray[cyx] (3, 600, 546)
├── Shapes
│ └── 'GSM7968253_NL15': GeoDataFrame shape: (1729, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1729, 17943)
with coordinate systems:
▸ 'GSM7968253_NL15', with elements:
GSM7968253_NL15_hires_image (Images), GSM7968253_NL15_lowres_image (Images), GSM7968253_NL15 (Shapes)
▸ 'GSM7968253_NL15_downscaled_hires', with elements:
GSM7968253_NL15_hires_image (Images), GSM7968253_NL15 (Shapes)
▸ 'GSM7968253_NL15_downscaled_lowres', with elements:
GSM7968253_NL15_lowres_image (Images), GSM7968253_NL15 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("XH9TqXgqtlou8Mik0000")
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("XH9TqXgqtlou8Mik") # 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 XH9TqXgqtlou8Mik0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/XH9TqXgqtlou8Mik
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid XH9TqXgqtlou8MikLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics of primary human hepatoblastomas→ 3 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- liver
- Modality
- RNA
- Observations (spots)
- 1,729
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,819 × 2,000 px
- mpp
- 4.048 µm/px
- Size
- 6.2 MB
- Sample ID
- GSM7968253
- License
- NCBI GEO policy
- Published
- Sep 12, 2024
Cite this dataset
doi.org/10.1038/s41467-024-53802-4 ↗ BibTeX
@article{Wu_2024,
title = {A developmental biliary lineage program cooperates with Wnt activation to promote cell proliferation in hepatoblastoma},
volume = {15},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-024-53802-4},
DOI = {10.1038/s41467-024-53802-4},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Wu, Peng V. and Fish, Matt and Hazard, Florette K. and Zhu, Chunfang and Vennam, Sujay and Walton, Hannah and Wagh, Dhananjay and Coller, John and Przybyl, Joanna and Morri, Maurizio and Neff, Norma and West, Robert B. and Nusse, Roel},
year = {2024},
month = Nov
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB