10x Xenium
Human bone marrow
GSM8386297
bronze Interactive viewer myelodysplastic syndrome Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 20520, 28471), (1, 10260, 14235), (1, 5130, 7117), (1, 2565, 3558), (1, 1282, 1779)
│ └── 'morphology_mip': DataTree[cyx] (1, 20520, 28471), (1, 10260, 14235), (1, 5130, 7117), (1, 2565, 3558), (1, 1282, 1779)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (20440, 27299), (10220, 13649), (5110, 6824), (2555, 3412), (1277, 1706)
│ └── 'nucleus_labels': DataTree[yx] (20300, 27198), (10150, 13599), (5075, 6799), (2537, 3399), (1268, 1699)
├── Points
│ └── 'transcripts': DataFrame with shape: (7307500, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (38492, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (38492, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (38492, 2) (2D shapes)
└── Tables
└── 'table': AnnData (38492, 471)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (Images), morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("iGXQqsoMUFfZkbWP") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/iGXQqsoMUFfZkbWP
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid iGXQqsoMUFfZkbWP Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["iGXQqsoMUFfZkbWP0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
High resolution mapping of erythroid niches in human using subcellular spatial transcriptomics→ 3 datasets · publication
Metadata
- Technology
- 10x Xenium
- Organism
- human
- Tissue
- bone marrow
- Condition
- myelodysplastic syndrome
- Modality
- RNA
- Observations
- 38,492
- Transcripts
- 7,307,500
- Tier
- bronze
- Size
- 1.4 GB
- Sample ID
- GSM8386297
- License
- NCBI GEO policy
- Published
- May 18, 2026
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB