10x Xenium
Human bone marrow
GSM9035040
bronze Interactive viewer smoldering plasma cell myeloma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 54408, 14406), (1, 27204, 7203), (1, 13602, 3601), (1, 6801, 1800), (1, 3400, 900)
├── Labels
│ └── 'cell_labels': DataTree[yx] (53901, 12974), (26950, 6487), (13475, 3243), (6737, 1621), (3368, 810)
├── Points
│ └── 'transcripts': DataFrame with shape: (8020527, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (89052, 1) (2D shapes)
│ └── 'cell_circles': GeoDataFrame shape: (89052, 2) (2D shapes)
└── Tables
└── 'table': AnnData (89052, 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("pNjYFlbaUh3FuzoS0000")
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("pNjYFlbaUh3FuzoS") # 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 pNjYFlbaUh3FuzoS0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pNjYFlbaUh3FuzoS
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pNjYFlbaUh3FuzoSLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- bone marrow
- Condition
- smoldering plasma cell myeloma
- Modality
- RNA
- Observations (cells)
- 89,052
- Transcripts
- 8,020,527
- Tier
- bronze
- Size
- 1.0 GB
- Sample ID
- GSM9035040
- License
- NCBI GEO policy
- Published
- Jul 13, 2025
Cite this dataset
doi.org/10.1182/blood.2025028896 ↗ BibTeX
@article{geo:GSM9035040,
doi = {10.1182/blood.2025028896},
title = {GSM9035040},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB