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Visium

Mouse mucosa of oral region

GSM8745173

bronze Interactive viewer H&E Provisional
Mouse mucosa of oral region preview
print(sdata) 
SpatialData object
├── Images
│     ├── 'GSM8745173_OM_UW_hires_image': DataArray[cyx] (3, 1968, 2000)
│     └── 'GSM8745173_OM_UW_lowres_image': DataArray[cyx] (3, 591, 600)
├── Shapes
│     └── 'GSM8745173_OM_UW': GeoDataFrame shape: (1288, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1288, 32285)
with coordinate systems:
    ▸ 'GSM8745173_OM_UW', with elements:
        GSM8745173_OM_UW_hires_image (Images), GSM8745173_OM_UW_lowres_image (Images), GSM8745173_OM_UW (Shapes)
    ▸ 'GSM8745173_OM_UW_downscaled_hires', with elements:
        GSM8745173_OM_UW_hires_image (Images), GSM8745173_OM_UW (Shapes)
    ▸ 'GSM8745173_OM_UW_downscaled_lowres', with elements:
        GSM8745173_OM_UW_lowres_image (Images), GSM8745173_OM_UW (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("kWYZEhjaCSjENv8U0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)
Install (Python 3.12+) Docs →
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("kWYZEhjaCSjENv8U")   # 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
Install (Python 3.12+) Docs →
Shell 
# sddb client: download the .zarr into data/
sddb-cli download kWYZEhjaCSjENv8U0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/kWYZEhjaCSjENv8U

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid kWYZEhjaCSjENv8U
Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue
Part of collection
Gas6-Axl signaling drives oral regenerative wound repair→
4 datasets · comparison

Metadata

Technology
Visium
Organism
mouse
Tissue
mucosa of oral region
Modality
RNA
Observations (spots)
1,288
Tier
bronze
Chemistry
Visium v1
Magnification
other
Resolution
2,000 × 1,968 px
mpp
3.680 µm/px
Size
11.3 MB
Sample ID
GSM8745173
License
NCBI GEO policy
Published
Apr 30, 2025

Cite this dataset

doi.org/10.1126/scitranslmed.adk2101 ↗
BibTeX 
@article{Griffin_2025,
  title = {Growth arrest specific–6 and angiotoxin receptor–like signaling drive oral regenerative wound repair},
  volume = {17},
  ISSN = {1946-6242},
  url = {http://dx.doi.org/10.1126/scitranslmed.adk2101},
  DOI = {10.1126/scitranslmed.adk2101},
  number = {805},
  journal = {Science Translational Medicine},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {Griffin, Michelle F. and Cook, Jessica and Morgan, Annah and Boffelli, Dario and Downer, Mauricio and Spielman, Amanda F. and Guardino, Nicholas J. and Guo, Jason L. and Parker, Jennifer B. L. and Januszyk, Michael and Valencia, Caleb and Kuhnert, Maxwell and Lu, John and Zwick, Rachel and Wan, Derrick C. and Klein, Ophir D. and Longaker, Michael T.},
  year = {2025},
  month = July
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB