10x Xenium

Mouse heart left ventricle

GSM8595805

bronze Interactive viewer heart disorder Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Labels
│     ├── 'cell_labels': DataTree[yx] (22660, 25268), (11330, 12634), (5665, 6317), (2832, 3158), (1416, 1579)
│     └── 'nucleus_labels': DataTree[yx] (22521, 24950), (11260, 12475), (5630, 6237), (2815, 3118), (1407, 1559)
├── Points
│     └── 'transcripts': DataFrame with shape: (8131244, 11) (3D points)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (35946, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (35946, 2) (2D shapes)
│     └── 'nucleus_boundaries': GeoDataFrame shape: (35495, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (35946, 475)
with coordinate systems:
    ▸ 'global', with elements:
        cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("xVmrmiGLWJbZ0qzQ0000")
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("xVmrmiGLWJbZ0qzQ")   # 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 xVmrmiGLWJbZ0qzQ0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/xVmrmiGLWJbZ0qzQ

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid xVmrmiGLWJbZ0qzQ

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Spatiotemporal dynamics of the cardioimmune niche during lesion repair [spatial]→

7 datasets · comparison

Metadata

Technology: 10x Xenium
Organism: mouse
Tissue: heart left ventricle
Condition: heart disorder
Modality: RNA
Observations (cells): 35,946
Transcripts: 8,131,244
Tier: bronze
Size: 382 MB
Sample ID: GSM8595805
License: NCBI GEO policy
Published: Sep 22, 2025

Cite this dataset

doi.org/10.1038/s44161-025-00739-6 ↗

BibTeX

@article{geo:GSM8595805,
  doi = {10.1038/s44161-025-00739-6},
  title = {GSM8595805},
  year = {2025}
}

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