10x Xenium
Human bone marrow
GSM10001173
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataTree[cyx] (1, 95126, 51095), (1, 47563, 25547), (1, 23781, 12773), (1, 11890, 6386), (1, 5945, 3193)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (94964, 49766), (47482, 24883), (23741, 12441), (11870, 6220), (5935, 3110)
│ └── 'nucleus_labels': DataTree[yx] (94917, 49719), (47458, 24859), (23729, 12429), (11864, 6214), (5932, 3107)
├── Points
│ └── 'transcripts': DataFrame with shape: (7401748, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (435167, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (435167, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (435167, 2) (2D shapes)
└── Tables
└── 'table': AnnData (435167, 480)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("OSIqs9TPBdY8reQj0000")
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("OSIqs9TPBdY8reQj") # 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 OSIqs9TPBdY8reQj0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/OSIqs9TPBdY8reQj
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid OSIqs9TPBdY8reQjLicense: NCBI GEO policy
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- bone marrow
- Modality
- RNA
- Observations (cells)
- 435,167
- Transcripts
- 7,401,748
- Tier
- bronze
- Size
- 5.3 GB
- Sample ID
- GSM10001173
- License
- NCBI GEO policy
- Published
- Aug 28, 2026
Cite this dataset
doi.org/10.1158/2643-3230.BCD-26-0080 ↗ BibTeX
@article{geo:GSM10001173,
doi = {10.1158/2643-3230.BCD-26-0080},
title = {GSM10001173},
year = {2026}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB