Visium
Mouse popliteal lymph node
GSM5841553
bronze Interactive viewer H&E rheumatoid arthritis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5841553_Adv2_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM5841553_Adv2_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM5841553_Adv2': GeoDataFrame shape: (1782, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1782, 32287)
with coordinate systems:
▸ 'GSM5841553_Adv2', with elements:
GSM5841553_Adv2_hires_image (Images), GSM5841553_Adv2_lowres_image (Images), GSM5841553_Adv2 (Shapes)
▸ 'GSM5841553_Adv2_downscaled_hires', with elements:
GSM5841553_Adv2_hires_image (Images), GSM5841553_Adv2 (Shapes)
▸ 'GSM5841553_Adv2_downscaled_lowres', with elements:
GSM5841553_Adv2_lowres_image (Images), GSM5841553_Adv2 (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("q7sdzoWgTv0pz6KO") # 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/q7sdzoWgTv0pz6KO
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid q7sdzoWgTv0pz6KO Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["q7sdzoWgTv0pz6KO0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial Transcriptomics of Joint-Draining Popliteal Lymph Nodes from Wild-type and TNF-Tg Mice with Early and Advanced Inflammatory-Erosive Arthritis→ 4 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- popliteal lymph node
- Condition
- rheumatoid arthritis
- Modality
- RNA
- Observations
- 1,782
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 2,000 px
- mpp
- 3.290 µm/px
- Size
- 9.8 MB
- Sample ID
- GSM5841553
- License
- unknown
- Published
- Aug 14, 2023
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · Reprocessed to SpatialData by SpatialData-DB