Visium
Human liver
GSM8041062
bronze Interactive viewer H&E colorectal cancer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8041062_CLM_02_hires_image': DataArray[cyx] (3, 2000, 1946)
│ └── 'GSM8041062_CLM_02_lowres_image': DataArray[cyx] (3, 600, 584)
├── Shapes
│ └── 'GSM8041062_CLM_02': GeoDataFrame shape: (3070, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3070, 17943)
with coordinate systems:
▸ 'GSM8041062_CLM_02', with elements:
GSM8041062_CLM_02_hires_image (Images), GSM8041062_CLM_02_lowres_image (Images), GSM8041062_CLM_02 (Shapes)
▸ 'GSM8041062_CLM_02_downscaled_hires', with elements:
GSM8041062_CLM_02_hires_image (Images), GSM8041062_CLM_02 (Shapes)
▸ 'GSM8041062_CLM_02_downscaled_lowres', with elements:
GSM8041062_CLM_02_lowres_image (Images), GSM8041062_CLM_02 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("OPuG41NCPaORKZYg") # 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/OPuG41NCPaORKZYg
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid OPuG41NCPaORKZYg Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["OPuG41NCPaORKZYg0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
High-resolution analysis of mononuclear phagocytes reveals clinically relevant markers in human colo-rectal liver metastasis - Visium Spatial Transcriptomics→ 2 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- liver
- Condition
- colorectal cancer
- Modality
- RNA
- Observations
- 3,070
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,946 × 2,000 px
- mpp
- 3.352 µm/px
- Size
- 39 MB
- Sample ID
- GSM8041062
- License
- unknown
- Published
- Jan 29, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB