Visium
Mouse small intestine
GSM7106694
silver Interactive viewer H&E No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs_hires_image': DataArray[cyx] (3, 2000, 1979)
│ └── 'GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs_lowres_image': DataArray[cyx] (3, 600, 594)
├── Shapes
│ └── 'GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs': GeoDataFrame shape: (4859, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4859, 32285)
with coordinate systems:
▸ 'GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs', with elements:
GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs_hires_image (Images), GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs_lowres_image (Images), GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs (Shapes)
▸ 'GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs_downscaled_hires', with elements:
GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs_hires_image (Images), GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs (Shapes)
▸ 'GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs_downscaled_lowres', with elements:
GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs_lowres_image (Images), GSM7106694_STD_irrad3_Volumes_jenfra_Private_Projects_Das_visium_irradiation_GEO_upload_outs_STD_irrad3_outs (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("UNN2r1eB9bS8SIx60000")
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("UNN2r1eB9bS8SIx6") # 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 UNN2r1eB9bS8SIx60000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/UNN2r1eB9bS8SIx6
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid UNN2r1eB9bS8SIx6License: NCBI GEO policy
Part of collection
Time-series spatial transcriptomic analysis of murine small intestine (SI) undergoing irradiation induced injury-repair with and without LXR activation→ 4 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- small intestine
- Modality
- RNA
- Observations (spots)
- 4,859
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 1,979 × 2,000 px
- mpp
- 3.507 µm/px
- Size
- 64.7 MB
- Sample ID
- GSM7106694
- License
- NCBI GEO policy
- Published
- Jul 19, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB