Visium HD

Mouse neocortex

GSM10119717

silver Interactive viewer H&E Smith-Magenis syndrome No linked publication

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print(sdata)

SpatialData object
├── Images
│     ├── 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_hires_image': DataArray[cyx] (3, 6000, 5296)
│     └── 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_lowres_image': DataArray[cyx] (3, 600, 530)
├── Shapes
│     ├── 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_002um': GeoDataFrame shape: (5406848, 1) (2D shapes)
│     ├── 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_008um': GeoDataFrame shape: (337928, 1) (2D shapes)
│     ├── 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_016um': GeoDataFrame shape: (84918, 1) (2D shapes)
│     └── 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_016um_for_vitessce': GeoDataFrame shape: (84918, 2) (2D shapes)
└── Tables
      ├── 'square_002um': AnnData (5406848, 19059)
      ├── 'square_008um': AnnData (337928, 19059)
      └── 'square_016um': AnnData (84918, 19059)
with coordinate systems:
    ▸ 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um', with elements:
        GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_hires_image (Images), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_lowres_image (Images), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_002um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_008um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_016um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_016um_for_vitessce (Shapes)
    ▸ 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_downscaled_hires', with elements:
        GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_hires_image (Images), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_002um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_008um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_016um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_016um_for_vitessce (Shapes)
    ▸ 'GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_downscaled_lowres', with elements:
        GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_lowres_image (Images), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_002um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_008um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_016um (Shapes), GSM10119717_SMS_D1_spaceranger_processed_SMS_D1_spaceranger_processed_binned_outputs_square_002um_square_016um_for_vitessce (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("dMnXGWHj1qV0Rm6t0000")
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("dMnXGWHj1qV0Rm6t")   # 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 dMnXGWHj1qV0Rm6t0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/dMnXGWHj1qV0Rm6t

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid dMnXGWHj1qV0Rm6t

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

geo-gse350715→

1 datasets · other

Metadata

Technology: Visium HD
Vendor: 10x Genomics
Organism: mouse
Tissue: neocortex
Condition: Smith-Magenis syndrome
Modality: RNA
Observations (bins): 337,928
Tier: silver
Resolution: 5,296 × 6,000 px
mpp: 1.321 µm/px
Size: 1.1 GB
Sample ID: GSM10119717
License: NCBI GEO policy
Published: Oct 18, 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