Visium

Mouse bone tissue

GSM9564258

bronze Interactive viewer H&E lung carcinoma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM9564258_Bone_ST_24667_hires_image': DataArray[cyx] (3, 2000, 1865)
│     └── 'GSM9564258_Bone_ST_24667_lowres_image': DataArray[cyx] (3, 600, 560)
├── Shapes
│     └── 'GSM9564258_Bone_ST_24667': GeoDataFrame shape: (2153, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2153, 32285)
with coordinate systems:
    ▸ 'GSM9564258_Bone_ST_24667', with elements:
        GSM9564258_Bone_ST_24667_hires_image (Images), GSM9564258_Bone_ST_24667_lowres_image (Images), GSM9564258_Bone_ST_24667 (Shapes)
    ▸ 'GSM9564258_Bone_ST_24667_downscaled_hires', with elements:
        GSM9564258_Bone_ST_24667_hires_image (Images), GSM9564258_Bone_ST_24667 (Shapes)
    ▸ 'GSM9564258_Bone_ST_24667_downscaled_lowres', with elements:
        GSM9564258_Bone_ST_24667_lowres_image (Images), GSM9564258_Bone_ST_24667 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("4x2FaJBWCBSjtaxk0001")
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("4x2FaJBWCBSjtaxk")   # 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 4x2FaJBWCBSjtaxk0001 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/4x2FaJBWCBSjtaxk

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 4x2FaJBWCBSjtaxk

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Single-cell and Spatial Transcriptomic Profiling of the Bone Metastatic Microenvironment→

4 datasets · other

Metadata

Technology: Visium
Organism: mouse
Tissue: bone tissue
Condition: lung carcinoma
Modality: RNA
Observations (spots): 2,153
Tier: bronze
Chemistry: Visium v1
Resolution: 1,865 × 2,000 px
mpp: 3.921 µm/px
Size: 26.5 MB
Sample ID: GSM9564258
License: NCBI GEO policy
Published: Mar 11, 2026

Cite this dataset

doi.org/10.1038/s41392-026-02691-8 ↗

BibTeX

@article{geo:GSE323357,
  doi = {10.1038/s41392-026-02691-8},
  title = {GSM9564257},
  year = {2026}
}

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