10x Xenium

Human bone marrow

GSM9035044

bronze Interactive viewer plasma cell myeloma Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'morphology_mip': DataTree[cyx] (1, 23901, 14308), (1, 11950, 7154), (1, 5975, 3577), (1, 2987, 1788), (1, 1493, 894)
├── Labels
│     └── 'cell_labels': DataTree[yx] (21790, 13931), (10895, 6965), (5447, 3482), (2723, 1741), (1361, 870)
├── Points
│     └── 'transcripts': DataFrame with shape: (1207355, 10) (3D points)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (54315, 1) (2D shapes)
│     └── 'cell_circles': GeoDataFrame shape: (54315, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (54315, 377)
with coordinate systems:
    ▸ 'global', with elements:
        morphology_mip (Images), cell_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("9R6FDWynoKd3LhXz0000")
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("9R6FDWynoKd3LhXz")   # 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 9R6FDWynoKd3LhXz0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/9R6FDWynoKd3LhXz

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 9R6FDWynoKd3LhXz

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Metadata

Technology: 10x Xenium
Organism: human
Tissue: bone marrow
Condition: plasma cell myeloma
Modality: RNA
Observations (cells): 54,315
Transcripts: 1,207,355
Tier: bronze
Size: 456 MB
Sample ID: GSM9035044
License: NCBI GEO policy
Published: Jul 13, 2025

Cite this dataset

doi.org/10.1182/blood.2025028896 ↗

BibTeX

@article{geo:GSM9035044,
  doi = {10.1182/blood.2025028896},
  title = {GSM9035044},
  year = {2025}
}

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