10x Xenium
Mouse buccal mucosa
GSM8586922
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (75819, 20137), (37909, 10068), (18954, 5034), (9477, 2517), (4738, 1258)
│ └── 'nucleus_labels': DataTree[yx] (75729, 19997), (37864, 9998), (18932, 4999), (9466, 2499), (4733, 1249)
├── Points
│ └── 'transcripts': DataFrame with shape: (11636230, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (67803, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (67803, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (67803, 1) (2D shapes)
└── Tables
└── 'table': AnnData (67803, 328)
with coordinate systems:
▸ 'global', with elements:
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("sEbDR3aWnrOwTiMA0000")
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("sEbDR3aWnrOwTiMA") # 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 sEbDR3aWnrOwTiMA0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/sEbDR3aWnrOwTiMA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid sEbDR3aWnrOwTiMALicense: NCBI GEO policy
Part of collection
Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [Xenium]→ 4 datasets · comparison
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- buccal mucosa
- Modality
- RNA
- Observations (cells)
- 67,803
- Transcripts
- 11,636,230
- Tier
- bronze
- Size
- 548 MB
- Sample ID
- GSM8586922
- License
- NCBI GEO policy
- Published
- Nov 22, 2024
Cite this dataset
doi.org/10.1172/jci.insight.182844 ↗ BibTeX
@article{geo:GSM8586922,
doi = {10.1172/jci.insight.182844},
title = {GSM8586922},
year = {2024}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB