Visium

Human skin of body

GSM8656737

silver Interactive viewer H&E peripheral T-cell lymphoma, not otherwise specified No linked publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8656737_H21088-21_Sonden_SpikeIn_hires_image': DataArray[cyx] (3, 2000, 2000)
│     └── 'GSM8656737_H21088-21_Sonden_SpikeIn_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│     └── 'GSM8656737_H21088-21_Sonden_SpikeIn': GeoDataFrame shape: (793, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (793, 17944)
with coordinate systems:
    ▸ 'GSM8656737_H21088-21_Sonden_SpikeIn', with elements:
        GSM8656737_H21088-21_Sonden_SpikeIn_hires_image (Images), GSM8656737_H21088-21_Sonden_SpikeIn_lowres_image (Images), GSM8656737_H21088-21_Sonden_SpikeIn (Shapes)
    ▸ 'GSM8656737_H21088-21_Sonden_SpikeIn_downscaled_hires', with elements:
        GSM8656737_H21088-21_Sonden_SpikeIn_hires_image (Images), GSM8656737_H21088-21_Sonden_SpikeIn (Shapes)
    ▸ 'GSM8656737_H21088-21_Sonden_SpikeIn_downscaled_lowres', with elements:
        GSM8656737_H21088-21_Sonden_SpikeIn_lowres_image (Images), GSM8656737_H21088-21_Sonden_SpikeIn (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("L6LtkBrwVt5Y5qkm0000")
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("L6LtkBrwVt5Y5qkm")   # 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 L6LtkBrwVt5Y5qkm0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/L6LtkBrwVt5Y5qkm

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid L6LtkBrwVt5Y5qkm

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Multi-Omic Single-Cell Dissection of Leukemic T-Cell Lymphoma Following CAR T-Cell Therapy [Spatial Transcriptomics]→

3 datasets · comparison

Metadata

Technology: Visium
Organism: human
Tissue: skin of body
Condition: peripheral T-cell lymphoma, not otherwise specified
Modality: RNA
Observations (spots): 793
Tier: silver
Chemistry: Visium v1
Resolution: 2,000 × 2,000 px
mpp: 3.651 µm/px
Size: 10.3 MB
Sample ID: GSM8656737
License: NCBI GEO policy
Published: Jan 5, 2025

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