Visium

Mouse brain

GSM9517484

silver Interactive viewer H&E traumatic brain injury ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM9517484_P3-60806_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│     ├── 'GSM9517484_P3-60806_hires_image': DataArray[cyx] (3, 2000, 1339)
│     └── 'GSM9517484_P3-60806_lowres_image': DataArray[cyx] (3, 600, 402)
├── Shapes
│     └── 'GSM9517484_P3-60806': GeoDataFrame shape: (3679, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (3679, 19465)
with coordinate systems:
    ▸ 'GSM9517484_P3-60806', with elements:
        GSM9517484_P3-60806_full_image (Images), GSM9517484_P3-60806_hires_image (Images), GSM9517484_P3-60806_lowres_image (Images), GSM9517484_P3-60806 (Shapes)
    ▸ 'GSM9517484_P3-60806_downscaled_hires', with elements:
        GSM9517484_P3-60806_hires_image (Images), GSM9517484_P3-60806 (Shapes)
    ▸ 'GSM9517484_P3-60806_downscaled_lowres', with elements:
        GSM9517484_P3-60806_lowres_image (Images), GSM9517484_P3-60806 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("lIZWVvx4CkeUOkiJ0000")
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("lIZWVvx4CkeUOkiJ")   # 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 lIZWVvx4CkeUOkiJ0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/lIZWVvx4CkeUOkiJ

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid lIZWVvx4CkeUOkiJ

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Mapping the Secondary Response to Traumatic Brain Injury Using Spatial Transcriptomics Shows Acute 4-aminopyridine Treatment Mitigates Axonal and Molecular Pathology→

24 datasets · comparison

Metadata

Technology: Visium
Organism: mouse
Tissue: brain
Condition: traumatic brain injury
Modality: RNA
Observations (spots): 3,679
Tier: silver
Chemistry: Visium CytAssist v2
Resolution: 1,339 × 2,000 px
mpp: 3.718 µm/px
Size: 136 MB
Sample ID: GSM9517484
License: NCBI GEO policy
Published: Feb 12, 2026

Cite this dataset

doi.org/10.1186/s40478-025-02219-1 ↗

BibTeX

@article{Sullivan_2026,
  title = {Mapping the secondary response to traumatic brain injury using spatial transcriptomics shows acute 4-aminopyridine treatment mitigates axonal and molecular pathology},
  volume = {14},
  ISSN = {2051-5960},
  url = {http://dx.doi.org/10.1186/s40478-025-02219-1},
  DOI = {10.1186/s40478-025-02219-1},
  number = {1},
  journal = {Acta Neuropathologica Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Sullivan, Genevieve M. and Radomski, Kryslaine L. and He, Shaoqiu and Wilkerson, Matthew D. and Dalgard, Clifton L. and Alba, Camille and Zi, Xiaomei and Doughty, Martin L. and Armstrong, Regina C.},
  year = {2026},
  month = Jan
}

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