Visium

Mouse brain

GSM9367541

bronze Interactive viewer H&E traumatic brain injury Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM9367541_L0-37641_hires_image': DataArray[cyx] (3, 1959, 2000)
│     └── 'GSM9367541_L0-37641_lowres_image': DataArray[cyx] (3, 588, 600)
├── Shapes
│     └── 'GSM9367541_L0-37641': GeoDataFrame shape: (2459, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2459, 32285)
with coordinate systems:
    ▸ 'GSM9367541_L0-37641', with elements:
        GSM9367541_L0-37641_hires_image (Images), GSM9367541_L0-37641_lowres_image (Images), GSM9367541_L0-37641 (Shapes)
    ▸ 'GSM9367541_L0-37641_downscaled_hires', with elements:
        GSM9367541_L0-37641_hires_image (Images), GSM9367541_L0-37641 (Shapes)
    ▸ 'GSM9367541_L0-37641_downscaled_lowres', with elements:
        GSM9367541_L0-37641_lowres_image (Images), GSM9367541_L0-37641 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("MonDsh5ZQ1Lc3aET0000")
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("MonDsh5ZQ1Lc3aET")   # 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 MonDsh5ZQ1Lc3aET0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/MonDsh5ZQ1Lc3aET

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid MonDsh5ZQ1Lc3aET

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Adult Mouse Controlled Cortical Impact Visium Spatial Transcriptomics→

34 datasets · time course

Metadata

Technology: Visium
Organism: mouse
Tissue: brain
Condition: traumatic brain injury
Modality: RNA
Observations (spots): 2,459
Tier: bronze
Chemistry: Visium v1
Resolution: 2,000 × 1,959 px
mpp: 3.507 µm/px
Size: 48.1 MB
Sample ID: GSM9367541
License: NCBI GEO policy
Published: Dec 17, 2025

Cite this dataset

doi.org/10.1177/08977151251390528 ↗

BibTeX

@article{geo:GSM9367541,
  doi = {10.1177/08977151251390528},
  title = {GSM9367541},
  year = {2026}
}

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