10x Xenium
Mouse bone marrow
GSM8945654
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (4, 17112, 31294), (4, 8556, 15647), (4, 4278, 7823), (4, 2139, 3911), (4, 1069, 1955)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (17112, 31294), (8556, 15647), (4278, 7823), (2139, 3911), (1069, 1955)
│ └── 'nucleus_labels': DataTree[yx] (17112, 31294), (8556, 15647), (4278, 7823), (2139, 3911), (1069, 1955)
├── Points
│ └── 'transcripts': DataFrame with shape: (16579522, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (143810, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (143810, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (145965, 2) (2D shapes)
└── Tables
└── 'table': AnnData (143810, 5050)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (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("7I3adVcRwB2pKHDJ") # 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/7I3adVcRwB2pKHDJ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7I3adVcRwB2pKHDJ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["7I3adVcRwB2pKHDJ0000"])[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 mice using subcellular spatial transcriptomics→ 6 datasets · publication
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- bone marrow
- Modality
- RNA
- Observations
- 143,810
- Transcripts
- 16,579,522
- Tier
- bronze
- Size
- 1.9 GB
- Sample ID
- GSM8945654
- 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