Visium
Human liver
GSM7845915
bronze Interactive viewer H&E primary sclerosing cholangitis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7845915_PSC011_B1_VISIUM_hires_image': DataArray[cyx] (3, 1986, 2000)
│ └── 'GSM7845915_PSC011_B1_VISIUM_lowres_image': DataArray[cyx] (3, 596, 600)
├── Shapes
│ └── 'GSM7845915_PSC011_B1_VISIUM': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 36601)
with coordinate systems:
▸ 'GSM7845915_PSC011_B1_VISIUM', with elements:
GSM7845915_PSC011_B1_VISIUM_hires_image (Images), GSM7845915_PSC011_B1_VISIUM_lowres_image (Images), GSM7845915_PSC011_B1_VISIUM (Shapes)
▸ 'GSM7845915_PSC011_B1_VISIUM_downscaled_hires', with elements:
GSM7845915_PSC011_B1_VISIUM_hires_image (Images), GSM7845915_PSC011_B1_VISIUM (Shapes)
▸ 'GSM7845915_PSC011_B1_VISIUM_downscaled_lowres', with elements:
GSM7845915_PSC011_B1_VISIUM_lowres_image (Images), GSM7845915_PSC011_B1_VISIUM (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("Q3tfobvi18Q0uuRa0000")
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("Q3tfobvi18Q0uuRa") # 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 Q3tfobvi18Q0uuRa0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Q3tfobvi18Q0uuRa
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Q3tfobvi18Q0uuRaLicense: NCBI GEO policy
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
- Condition
- primary sclerosing cholangitis
- Modality
- RNA
- Observations (spots)
- 4,992
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,986 px
- mpp
- 3.358 µm/px
- Size
- 46.3 MB
- Sample ID
- GSM7845915
- License
- NCBI GEO policy
- 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 ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB