10x Xenium
Mouse brain
GSM9489189
silver Interactive viewer ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_focus': DataTree[cyx] (1, 13741, 17147), (1, 6870, 8573), (1, 3435, 4286), (1, 1717, 2143), (1, 858, 1071)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (13741, 17147), (6870, 8573), (3435, 4286), (1717, 2143), (858, 1071)
│ └── 'nucleus_labels': DataTree[yx] (13741, 17147), (6870, 8573), (3435, 4286), (1717, 2143), (858, 1071)
├── Points
│ └── 'transcripts': DataFrame with shape: (11487027, 13) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (65647, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (65647, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (65647, 2) (2D shapes)
└── Tables
└── 'table': AnnData (65647, 347)
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("wJOfdI4qQQSLm6mj") # 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/wJOfdI4qQQSLm6mj
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid wJOfdI4qQQSLm6mj Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["wJOfdI4qQQSLm6mj0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Single-cell multiomic approaches define a gradual, spatially-regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells [Xenium]→ 10 datasets · comparison
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations
- 65,647
- Transcripts
- 11,487,027
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 669 MB
- Sample ID
- GSM9489189
- License
- NCBI GEO policy
- Published
- Jun 18, 2026
Cite this dataset
doi.org/10.1016/j.stemcr.2026.102967 ↗ BibTeX
@article{Wang_2026,
title = {Single-cell multiomic approaches define a gradual, spatially regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells},
volume = {21},
ISSN = {2213-6711},
url = {http://dx.doi.org/10.1016/j.stemcr.2026.102967},
DOI = {10.1016/j.stemcr.2026.102967},
number = {7},
journal = {Stem Cell Reports},
publisher = {Elsevier BV},
author = {Wang, Beatrix S. and Karamboulas, Konstantina and Tahmasian, Nareh and Dennis, Daniel J. and Kaplan, David R. and Miller, Freda D.},
year = {2026},
month = July,
pages = {102967}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB