Visium
Mouse spleen
GSM6042727
bronze Interactive viewer H&E lymphocytic choriomeningitis Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM6042727_Round1_B1_Day7_CD4depl_hires_image': DataArray[cyx] (3, 1987, 2000)
├── Shapes
│ └── 'GSM6042727_Round1_B1_Day7_CD4depl': GeoDataFrame shape: (2177, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2177, 32285)
with coordinate systems:
▸ 'GSM6042727_Round1_B1_Day7_CD4depl', with elements:
GSM6042727_Round1_B1_Day7_CD4depl_hires_image (Images), GSM6042727_Round1_B1_Day7_CD4depl (Shapes)
▸ 'GSM6042727_Round1_B1_Day7_CD4depl_downscaled_hires', with elements:
GSM6042727_Round1_B1_Day7_CD4depl_hires_image (Images), GSM6042727_Round1_B1_Day7_CD4depl (Shapes)
▸ 'GSM6042727_Round1_B1_Day7_CD4depl_downscaled_lowres', with elements:
GSM6042727_Round1_B1_Day7_CD4depl (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("f4JFyttSMJgv3rVZ") # 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/f4JFyttSMJgv3rVZ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid f4JFyttSMJgv3rVZ Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["f4JFyttSMJgv3rVZ0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial RNA-sequencing of day7 and day 21 post-LCMV Cl13 infection following transient CD4+ T cell depletion (Visium)→ 8 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- spleen
- Condition
- lymphocytic choriomeningitis
- Modality
- RNA
- Observations
- 2,177
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,987 px
- mpp
- 3.513 µm/px
- Size
- 35 MB
- Sample ID
- GSM6042727
- License
- unknown
- Published
- Nov 29, 2022
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB