Visium

Mouse liver

GSM8285401

bronze Interactive viewer H&E malaria Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8285401_C1_hires_image': DataArray[cyx] (3, 2000, 1979)
│     └── 'GSM8285401_C1_lowres_image': DataArray[cyx] (3, 600, 594)
├── Shapes
│     └── 'GSM8285401_C1': GeoDataFrame shape: (2999, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2999, 60646)
with coordinate systems:
    ▸ 'GSM8285401_C1', with elements:
        GSM8285401_C1_hires_image (Images), GSM8285401_C1_lowres_image (Images), GSM8285401_C1 (Shapes)
    ▸ 'GSM8285401_C1_downscaled_hires', with elements:
        GSM8285401_C1_hires_image (Images), GSM8285401_C1 (Shapes)
    ▸ 'GSM8285401_C1_downscaled_lowres', with elements:
        GSM8285401_C1_lowres_image (Images), GSM8285401_C1 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("uENTkIpHjr5exTbU0000")
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("uENTkIpHjr5exTbU")   # 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 uENTkIpHjr5exTbU0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/uENTkIpHjr5exTbU

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid uENTkIpHjr5exTbU

Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution (VISIUM)→

4 datasets · time course

Metadata

Technology: Visium
Organism: mouse
Tissue: liver
Condition: malaria
Modality: RNA
Observations (spots): 2,999
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 1,979 × 2,000 px
mpp: 3.503 µm/px
Size: 30.1 MB
Sample ID: GSM8285401
License: NCBI GEO policy
Published: Jun 3, 2024

Cite this dataset

doi.org/10.1038/s41467-024-51418-2 ↗

BibTeX

@article{Hildebrandt_2024,
  title = {Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution},
  volume = {15},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-024-51418-2},
  DOI = {10.1038/s41467-024-51418-2},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Hildebrandt, Franziska and Iturritza, Miren Urrutia and Zwicker, Christian and Vanneste, Bavo and Van Hul, Noémi and Semle, Elisa and Quin, Jaclyn and Pascini, Tales and Saarenpää, Sami and He, Mengxiao and Andersson, Emma R. and Scott, Charlotte L. and Vega-Rodriguez, Joel and Lundeberg, Joakim and Ankarklev, Johan},
  year = {2024},
  month = Aug
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB