10x Xenium
Human bone marrow
GSM9035024
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 13798, 42626), (1, 6899, 21313), (1, 3449, 10656), (1, 1724, 5328), (1, 862, 2664)
├── Labels
│ └── 'cell_labels': DataTree[yx] (13735, 42082), (6867, 21041), (3433, 10520), (1716, 5260), (858, 2630)
├── Points
│ └── 'transcripts': DataFrame with shape: (10944225, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (84790, 1) (2D shapes)
│ └── 'cell_circles': GeoDataFrame shape: (84790, 2) (2D shapes)
└── Tables
└── 'table': AnnData (84790, 5001)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("ezFkTKMfPp9WXMSh0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("ezFkTKMfPp9WXMSh") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download ezFkTKMfPp9WXMSh0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/ezFkTKMfPp9WXMSh
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ezFkTKMfPp9WXMShLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- bone marrow
- Modality
- RNA
- Observations (cells)
- 84,790
- Transcripts
- 10,944,225
- Tier
- bronze
- Size
- 954 MB
- Sample ID
- GSM9035024
- License
- NCBI GEO policy
- Published
- Jul 13, 2025
Cite this dataset
doi.org/10.1182/blood.2025028896 ↗ BibTeX
@article{geo:GSM9035024,
doi = {10.1182/blood.2025028896},
title = {GSM9035024},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB