Visium
Mouse mesenteric lymph node
GSM8131851
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8131851_09_IT15_AicdaWT_V11A27-336_A1_hires_image': DataArray[cyx] (4, 2000, 1948)
│ └── 'GSM8131851_09_IT15_AicdaWT_V11A27-336_A1_lowres_image': DataArray[cyx] (4, 600, 584)
├── Shapes
│ └── 'GSM8131851_09_IT15_AicdaWT_V11A27-336_A1': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 32589)
with coordinate systems:
▸ 'GSM8131851_09_IT15_AicdaWT_V11A27-336_A1', with elements:
GSM8131851_09_IT15_AicdaWT_V11A27-336_A1_hires_image (Images), GSM8131851_09_IT15_AicdaWT_V11A27-336_A1_lowres_image (Images), GSM8131851_09_IT15_AicdaWT_V11A27-336_A1 (Shapes)
▸ 'GSM8131851_09_IT15_AicdaWT_V11A27-336_A1_downscaled_hires', with elements:
GSM8131851_09_IT15_AicdaWT_V11A27-336_A1_hires_image (Images), GSM8131851_09_IT15_AicdaWT_V11A27-336_A1 (Shapes)
▸ 'GSM8131851_09_IT15_AicdaWT_V11A27-336_A1_downscaled_lowres', with elements:
GSM8131851_09_IT15_AicdaWT_V11A27-336_A1_lowres_image (Images), GSM8131851_09_IT15_AicdaWT_V11A27-336_A1 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("a2NXwr8AIlmfe5Fz") # 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/a2NXwr8AIlmfe5Fz
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid a2NXwr8AIlmfe5Fz Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["a2NXwr8AIlmfe5Fz0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Germinal Center Dark Zone harbors ATR-dependent determinants of T-cell exclusion that are also identified in aggressive lymphoma – Visium_FFPE_Spatial_Trasciptomics_project→ 2 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- mesenteric lymph node
- Modality
- RNA
- Observations
- 4,992
- Tier
- bronze
- Chemistry
- Visium v1
- Size
- 29 MB
- Sample ID
- GSM8131851
- License
- unknown
- Published
- Apr 17, 2024
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB