Visium HD

Human medial amygdaloid nucleus

GSM9937428

silver Interactive viewer H&E No linked publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM9937428_Br9280_MeA_hires_image': DataArray[cyx] (3, 6000, 3060)
│     └── 'GSM9937428_Br9280_MeA_lowres_image': DataArray[cyx] (3, 600, 306)
├── Shapes
│     ├── 'GSM9937428_Br9280_MeA_square_002um': GeoDataFrame shape: (11222500, 1) (2D shapes)
│     ├── 'GSM9937428_Br9280_MeA_square_008um': GeoDataFrame shape: (702244, 1) (2D shapes)
│     └── 'GSM9937428_Br9280_MeA_square_008um_for_vitessce': GeoDataFrame shape: (702244, 2) (2D shapes)
└── Tables
      ├── 'square_002um': AnnData (11222500, 37082)
      └── 'square_008um': AnnData (702244, 37082)
with coordinate systems:
    ▸ 'GSM9937428_Br9280_MeA', with elements:
        GSM9937428_Br9280_MeA_hires_image (Images), GSM9937428_Br9280_MeA_lowres_image (Images), GSM9937428_Br9280_MeA_square_002um (Shapes), GSM9937428_Br9280_MeA_square_008um (Shapes), GSM9937428_Br9280_MeA_square_008um_for_vitessce (Shapes)
    ▸ 'GSM9937428_Br9280_MeA_downscaled_hires', with elements:
        GSM9937428_Br9280_MeA_hires_image (Images), GSM9937428_Br9280_MeA_square_002um (Shapes), GSM9937428_Br9280_MeA_square_008um (Shapes), GSM9937428_Br9280_MeA_square_008um_for_vitessce (Shapes)
    ▸ 'GSM9937428_Br9280_MeA_downscaled_lowres', with elements:
        GSM9937428_Br9280_MeA_lowres_image (Images), GSM9937428_Br9280_MeA_square_002um (Shapes), GSM9937428_Br9280_MeA_square_008um (Shapes), GSM9937428_Br9280_MeA_square_008um_for_vitessce (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("qcdNHuIjzOkr9WB10000")
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("qcdNHuIjzOkr9WB1")   # 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 qcdNHuIjzOkr9WB10000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/qcdNHuIjzOkr9WB1

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid qcdNHuIjzOkr9WB1

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

geo-gse342738→

5 datasets · replicates

Metadata

Technology: Visium HD
Organism: human
Tissue: medial amygdaloid nucleus
Modality: RNA
Observations (bins): 702,244
Tier: silver
Resolution: 3,060 × 6,000 px
mpp: 3.271 µm/px
Size: 1.4 GB
Sample ID: GSM9937428
License: NCBI GEO policy
Published: Aug 24, 2026

Cite this dataset

No linked publication found — please cite the data source: NCBI GEO ↗.

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