Visium
Human brain
GSM8376640
bronze Interactive viewer H&E melanoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8376640_sample9_hires_image': DataArray[cyx] (3, 2000, 1946)
│ └── 'GSM8376640_sample9_lowres_image': DataArray[cyx] (3, 600, 584)
├── Shapes
│ └── 'GSM8376640_sample9': GeoDataFrame shape: (1302, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1302, 36601)
with coordinate systems:
▸ 'GSM8376640_sample9', with elements:
GSM8376640_sample9_hires_image (Images), GSM8376640_sample9_lowres_image (Images), GSM8376640_sample9 (Shapes)
▸ 'GSM8376640_sample9_downscaled_hires', with elements:
GSM8376640_sample9_hires_image (Images), GSM8376640_sample9 (Shapes)
▸ 'GSM8376640_sample9_downscaled_lowres', with elements:
GSM8376640_sample9_lowres_image (Images), GSM8376640_sample9 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Bo2o5ymAonNEV9Zh") # 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/Bo2o5ymAonNEV9Zh
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Bo2o5ymAonNEV9Zh Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Bo2o5ymAonNEV9Zh0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
spatialGE is a User-Friendly Web Application that Facilitates Spatial Transcriptomics Data Analysis→ 2 datasets · other
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- brain
- Condition
- melanoma
- Modality
- RNA
- Observations
- 1,302
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,946 × 2,000 px
- mpp
- 3.361 µm/px
- Size
- 9.1 MB
- Sample ID
- GSM8376640
- License
- unknown
- Published
- Nov 21, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB