Visium
Mouse colon
GSM5213483
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM5213483_V19S23-097_A1_S1_hires_image': DataArray[cyx] (3, 1804, 2000)
├── Shapes
│ └── 'GSM5213483_V19S23-097_A1_S1': GeoDataFrame shape: (2604, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2604, 31053)
with coordinate systems:
▸ 'GSM5213483_V19S23-097_A1_S1', with elements:
GSM5213483_V19S23-097_A1_S1_hires_image (Images), GSM5213483_V19S23-097_A1_S1 (Shapes)
▸ 'GSM5213483_V19S23-097_A1_S1_downscaled_hires', with elements:
GSM5213483_V19S23-097_A1_S1_hires_image (Images), GSM5213483_V19S23-097_A1_S1 (Shapes)
▸ 'GSM5213483_V19S23-097_A1_S1_downscaled_lowres', with elements:
GSM5213483_V19S23-097_A1_S1 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("3lrePYlDAF0nvPeJ") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/3lrePYlDAF0nvPeJ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 3lrePYlDAF0nvPeJ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["3lrePYlDAF0nvPeJ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
10X Visium Spatial transcriptomics of murine colon in steady state and during recovery after DSS colitis→ 2 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- colon
- Modality
- RNA
- Observations
- 2,604
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,804 px
- mpp
- 4.063 µm/px
- Size
- 45 MB
- Sample ID
- GSM5213483
- License
- unknown
- Published
- Dec 5, 2021
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB