Visium

Human amygdala

GSM9937029

silver Interactive viewer H&E No linked publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM9937029_Br6423-V13Y24-348_D1_full_image': DataTree[cyx] (3, 29582, 25831), (3, 14791, 12915), (3, 7395, 6457), (3, 3697, 3228), (3, 1848, 1614)
│     ├── 'GSM9937029_Br6423-V13Y24-348_D1_hires_image': DataArray[cyx] (3, 2000, 1747)
│     └── 'GSM9937029_Br6423-V13Y24-348_D1_lowres_image': DataArray[cyx] (3, 600, 524)
├── Shapes
│     └── 'GSM9937029_Br6423-V13Y24-348_D1': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4992, 36601)
with coordinate systems:
    ▸ 'GSM9937029_Br6423-V13Y24-348_D1', with elements:
        GSM9937029_Br6423-V13Y24-348_D1_full_image (Images), GSM9937029_Br6423-V13Y24-348_D1_hires_image (Images), GSM9937029_Br6423-V13Y24-348_D1_lowres_image (Images), GSM9937029_Br6423-V13Y24-348_D1 (Shapes)
    ▸ 'GSM9937029_Br6423-V13Y24-348_D1_downscaled_hires', with elements:
        GSM9937029_Br6423-V13Y24-348_D1_hires_image (Images), GSM9937029_Br6423-V13Y24-348_D1 (Shapes)
    ▸ 'GSM9937029_Br6423-V13Y24-348_D1_downscaled_lowres', with elements:
        GSM9937029_Br6423-V13Y24-348_D1_lowres_image (Images), GSM9937029_Br6423-V13Y24-348_D1 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("3mmDoy9m8FeUcoxj0000")
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("3mmDoy9m8FeUcoxj")   # 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 3mmDoy9m8FeUcoxj0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3mmDoy9m8FeUcoxj

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3mmDoy9m8FeUcoxj

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Multiscale spatial transcriptomics resolves the cellular and molecular architecture of the human amygdala [Visium]→

48 datasets · replicates

Metadata

Technology: Visium
Organism: human
Tissue: amygdala
Modality: RNA
Observations (spots): 4,992
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 25,831 × 29,582 px
mpp: 0.306 µm/px
Size: 1.8 GB
Sample ID: GSM9937029
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