Visium
Human pancreas
GSM8454388
bronze Interactive viewer H&E pancreatic ductal adenocarcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8454388_PDAC2_hires_image': DataArray[cyx] (3, 1859, 2000)
│ └── 'GSM8454388_PDAC2_lowres_image': DataArray[cyx] (3, 558, 600)
├── Shapes
│ └── 'GSM8454388_PDAC2': GeoDataFrame shape: (4118, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4118, 17943)
with coordinate systems:
▸ 'GSM8454388_PDAC2', with elements:
GSM8454388_PDAC2_hires_image (Images), GSM8454388_PDAC2_lowres_image (Images), GSM8454388_PDAC2 (Shapes)
▸ 'GSM8454388_PDAC2_downscaled_hires', with elements:
GSM8454388_PDAC2_hires_image (Images), GSM8454388_PDAC2 (Shapes)
▸ 'GSM8454388_PDAC2_downscaled_lowres', with elements:
GSM8454388_PDAC2_lowres_image (Images), GSM8454388_PDAC2 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("ht38hLfsxtvklzJt") # 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/ht38hLfsxtvklzJt
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ht38hLfsxtvklzJt Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ht38hLfsxtvklzJt0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Differential Activity of MAPK signalling Defines Fibroblast Subtypes in Pancreatic Cancer (Spatial Transcriptomics)→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- pancreas
- Condition
- pancreatic ductal adenocarcinoma
- Modality
- RNA
- Observations
- 4,118
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,859 px
- mpp
- 3.968 µm/px
- Size
- 61 MB
- Sample ID
- GSM8454388
- License
- unknown
- Published
- Dec 5, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB