10x Xenium
Mouse skin of back
GSM8586921
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Labels
│ ├── 'cell_labels': DataTree[yx] (67635, 29409), (33817, 14704), (16908, 7352), (8454, 3676), (4227, 1838)
│ └── 'nucleus_labels': DataTree[yx] (67528, 29269), (33764, 14634), (16882, 7317), (8441, 3658), (4220, 1829)
├── Points
│ └── 'transcripts': DataFrame with shape: (12046651, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (182402, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (182402, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (182402, 1) (2D shapes)
└── Tables
└── 'table': AnnData (182402, 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("CZ1cTOkiDCxOU1y40000")
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("CZ1cTOkiDCxOU1y4") # 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 CZ1cTOkiDCxOU1y40000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/CZ1cTOkiDCxOU1y4
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid CZ1cTOkiDCxOU1y4License: 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
- skin of back
- Modality
- RNA
- Observations (cells)
- 182,402
- Transcripts
- 12,046,651
- Tier
- bronze
- Size
- 673 MB
- Sample ID
- GSM8586921
- License
- NCBI GEO policy
- Published
- Nov 22, 2024
Cite this dataset
doi.org/10.1172/jci.insight.182844 ↗ BibTeX
@article{geo:GSM8586921,
doi = {10.1172/jci.insight.182844},
title = {GSM8586921},
year = {2024}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB