10x Xenium
Mouse forebrain
GSM8965606
silver Interactive viewer ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 30860, 39916), (1, 15430, 19958), (1, 7715, 9979), (1, 3857, 4989), (1, 1928, 2494)
│ └── 'morphology_mip': DataTree[cyx] (1, 30860, 39916), (1, 15430, 19958), (1, 7715, 9979), (1, 3857, 4989), (1, 1928, 2494)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30860, 39916), (15430, 19958), (7715, 9979), (3857, 4989), (1928, 2494)
│ └── 'nucleus_labels': DataTree[yx] (30860, 39916), (15430, 19958), (7715, 9979), (3857, 4989), (1928, 2494)
├── Points
│ └── 'transcripts': DataFrame with shape: (64484322, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (101394, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (101394, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (101394, 1) (2D shapes)
└── Tables
└── 'table': AnnData (101394, 347)
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) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("S58RknC54s6M26qX0000")
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("S58RknC54s6M26qX") # 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 S58RknC54s6M26qX0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/S58RknC54s6M26qX
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid S58RknC54s6M26qXLicense: NCBI GEO policy
Part of collection
Single cell approaches define the murine leptomeninges:cortical brain interface as a distinct cellular neighborhood comprised of neural and nonneural cell types→ 7 datasets · other
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- forebrain
- Modality
- RNA
- Observations (cells)
- 101,394
- Transcripts
- 64,484,322
- Tier
- silver
- Chemistry
- Xenium v1
- Size
- 6.0 GB
- Sample ID
- GSM8965606
- License
- NCBI GEO policy
- Published
- Aug 1, 2025
Cite this dataset
doi.org/10.1523/eneuro.0046-25.2025 ↗ BibTeX
@article{Ebert_2025,
title = {Single-Cell Approaches Define the Murine Leptomeninges: Cortical Brain Interface as a Distinct Cellular Neighborhood Composed of Neural and Non-neural Cell Types},
volume = {12},
ISSN = {2373-2822},
url = {http://dx.doi.org/10.1523/eneuro.0046-25.2025},
DOI = {10.1523/eneuro.0046-25.2025},
number = {8},
journal = {eneuro},
publisher = {Society for Neuroscience},
author = {Ebert, Sarah N. and Eisner, Christine and Karamboulas, Konstantina and Bernier, Louis-Philippe and Kaplan, David R. and MacVicar, Brian A. and Miller, Freda D.},
year = {2025},
month = Aug,
pages = {ENEURO.0046–25.2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB