Visium

Human liver

GSM7697869

bronze Provisional

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM7697869_C73B1_hires_image': DataArray[cyx] (4, 2000, 1963)
│     └── 'GSM7697869_C73B1_lowres_image': DataArray[cyx] (4, 600, 589)
├── Shapes
│     └── 'GSM7697869_C73B1': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4992, 36601)
with coordinate systems:
    ▸ 'GSM7697869_C73B1', with elements:
        GSM7697869_C73B1_hires_image (Images), GSM7697869_C73B1_lowres_image (Images), GSM7697869_C73B1 (Shapes)
    ▸ 'GSM7697869_C73B1_downscaled_hires', with elements:
        GSM7697869_C73B1_hires_image (Images), GSM7697869_C73B1 (Shapes)
    ▸ 'GSM7697869_C73B1_downscaled_lowres', with elements:
        GSM7697869_C73B1_lowres_image (Images), GSM7697869_C73B1 (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("0Er4Pnvi60YSgBFW")   # 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/0Er4Pnvi60YSgBFW

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 0Er4Pnvi60YSgBFW

Load with the Python client

# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["0Er4Pnvi60YSgBFW0001"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

View on Lamin ↗ Flag a data issue

Part of collection

Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver→

4 datasets · other

Metadata

Technology: Visium
Organism: human
Tissue: liver
Modality: RNA
Observations: 4,992
Tier: bronze
Chemistry: Visium v1
Size: 30 MB
Sample ID: GSM7697869
License: unknown
Published: Sep 26, 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 ↗ · Reprocessed to SpatialData by SpatialData-DB