Visium
Human lymph node
GSM8324906
silver Interactive viewer H&E diffuse large B-cell lymphoma No linked publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8324906_HLS_78_S1_hires_image': DataArray[cyx] (3, 1979, 2000)
│ └── 'GSM8324906_HLS_78_S1_lowres_image': DataArray[cyx] (3, 594, 600)
├── Shapes
│ └── 'GSM8324906_HLS_78_S1': GeoDataFrame shape: (349, 2) (2D shapes)
└── Tables
└── 'table': AnnData (349, 17943)
with coordinate systems:
▸ 'GSM8324906_HLS_78_S1', with elements:
GSM8324906_HLS_78_S1_hires_image (Images), GSM8324906_HLS_78_S1_lowres_image (Images), GSM8324906_HLS_78_S1 (Shapes)
▸ 'GSM8324906_HLS_78_S1_downscaled_hires', with elements:
GSM8324906_HLS_78_S1_hires_image (Images), GSM8324906_HLS_78_S1 (Shapes)
▸ 'GSM8324906_HLS_78_S1_downscaled_lowres', with elements:
GSM8324906_HLS_78_S1_lowres_image (Images), GSM8324906_HLS_78_S1 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("ou3nBG0bnwr8n6L2") # 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/ou3nBG0bnwr8n6L2
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid ou3nBG0bnwr8n6L2 Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["ou3nBG0bnwr8n6L20000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Patient-derived lymphomoids preserve the tumor architecture and allow testing response to therapies in lymphoma [Spatial Transcriptomics]→ 5 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lymph node
- Condition
- diffuse large B-cell lymphoma
- Modality
- RNA
- Observations
- 349
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,979 px
- mpp
- 3.320 µm/px
- Size
- 12 MB
- Sample ID
- GSM8324906
- License
- unknown
- Published
- Nov 26, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB