Visium

Mouse cerebral cortex

GSM7068163

bronze Interactive viewer H&E traumatic brain injury Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM7068163_A_hires_image': DataArray[cyx] (3, 2000, 2000)
│     └── 'GSM7068163_A_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│     └── 'GSM7068163_A': GeoDataFrame shape: (1740, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1740, 27998)
with coordinate systems:
    ▸ 'GSM7068163_A', with elements:
        GSM7068163_A_hires_image (Images), GSM7068163_A_lowres_image (Images), GSM7068163_A (Shapes)
    ▸ 'GSM7068163_A_downscaled_hires', with elements:
        GSM7068163_A_hires_image (Images), GSM7068163_A (Shapes)
    ▸ 'GSM7068163_A_downscaled_lowres', with elements:
        GSM7068163_A_lowres_image (Images), GSM7068163_A (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("87E1jHUh65FO9B4n0000")
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("87E1jHUh65FO9B4n")   # 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 87E1jHUh65FO9B4n0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/87E1jHUh65FO9B4n

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 87E1jHUh65FO9B4n

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Shared inflammatory glial cell signature after brain injury, revealed by spatial, temporal and cell-type-specific profiling of the murine cerebral cortex [spatial transcriptomics]→

2 datasets · time course

Metadata

Technology: Visium
Organism: mouse
Tissue: cerebral cortex
Condition: traumatic brain injury
Modality: RNA
Observations (spots): 1,740
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 2,000 px
mpp: 3.346 µm/px
Size: 31.5 MB
Sample ID: GSM7068163
License: NCBI GEO policy
Published: Aug 25, 2023

Cite this dataset

doi.org/10.1038/s41467-024-46625-w ↗

BibTeX

@article{Koupourtidou_2024,
  title = {Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex},
  volume = {15},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-024-46625-w},
  DOI = {10.1038/s41467-024-46625-w},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Koupourtidou, Christina and Schwarz, Veronika and Aliee, Hananeh and Frerich, Simon and Fischer-Sternjak, Judith and Bocchi, Riccardo and Simon-Ebert, Tatiana and Bai, Xianshu and Sirko, Swetlana and Kirchhoff, Frank and Dichgans, Martin and Götz, Magdalena and Theis, Fabian J. and Ninkovic, Jovica},
  year = {2024},
  month = Apr
}

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