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Visium

Human liver

NCBI674

silver Interactive viewer H&E primary sclerosing cholangitis ✓ Verified publication
Human liver preview
print(sdata) 
SpatialData object
├── Images
│     └── 'NCBI674_full_image': DataTree[cyx] (3, 25840, 25360), (3, 12920, 12680), (3, 6460, 6340), (3, 3230, 3170)
├── Shapes
│     └── 'NCBI674_spots': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4992, 36601)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI674_full_image (Images), NCBI674_spots (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("8jM9mtBYX9PZWuR90000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)
Install (Python 3.12+) Docs →
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("8jM9mtBYX9PZWuR9")   # 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
Install (Python 3.12+) Docs →
Shell 
# sddb client: download the .zarr into data/
sddb-cli download 8jM9mtBYX9PZWuR90000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/8jM9mtBYX9PZWuR9

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 8jM9mtBYX9PZWuR9
Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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Metadata

Technology
Visium
Organism
human
Tissue
liver
Condition
primary sclerosing cholangitis
Modality
RNA
Observations (spots)
4,992
Tier
silver
Chemistry
Visium v1
Magnification
20x
Resolution
25,360 × 25,840 px
mpp
0.304 µm/px
Size
1.5 GB
Sample ID
NCBI674
License
CC BY-NC-SA 4.0 NonCommercial
Published
Oct 6, 2023

Cite this dataset

doi.org/10.1016/j.jhep.2023.12.023 ↗
BibTeX 
@article{Andrews_2024,
  title = {Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver},
  volume = {80},
  ISSN = {0168-8278},
  url = {http://dx.doi.org/10.1016/j.jhep.2023.12.023},
  DOI = {10.1016/j.jhep.2023.12.023},
  number = {5},
  journal = {Journal of Hepatology},
  publisher = {Elsevier BV},
  author = {Andrews, Tallulah S. and Nakib, Diana and Perciani, Catia T. and Ma, Xue Zhong and Liu, Lewis and Winter, Erin and Camat, Damra and Chung, Sai W. and Lumanto, Patricia and Manuel, Justin and Mangroo, Shantel and Hansen, Bettina and Arpinder, Bal and Thoeni, Cornelia and Sayed, Blayne and Feld, Jordan and Gehring, Adam and Gulamhusein, Aliya and Hirschfield, Gideon M. and Ricciuto, Amanda and Bader, Gary D. and McGilvray, Ian D. and MacParland, Sonya},
  year = {2024},
  month = May,
  pages = {730–743}
}

Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB