Visium
Mouse intestine
NCBI685
silver Interactive viewer H&E ulcerative colitis No linked publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI685_full_image': DataTree[cyx] (3, 10194, 10502), (3, 5097, 5251), (3, 2548, 2625), (3, 1274, 1312)
├── Shapes
│ └── 'NCBI685_spots': GeoDataFrame shape: (3547, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3547, 31053)
with coordinate systems:
▸ 'global', with elements:
NCBI685_full_image (Images), NCBI685_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("yRsN116e2kAMfjLf0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) Python · lamindb
Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("yRsN116e2kAMfjLf") # stem uid: Lamin resolves it to the 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download yRsN116e2kAMfjLf0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/yRsN116e2kAMfjLf
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid yRsN116e2kAMfjLfLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
10X Visium Spatial transcriptomics of murine colon at d14 (mucosa healing) in B cell sufficient-deficient mice→ 2 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- intestine
- Condition
- ulcerative colitis
- Modality
- RNA
- Observations (spots)
- 3,547
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 10,502 × 10,194 px
- mpp
- 0.970 µm/px
- Size
- 339 MB
- Sample ID
- NCBI685
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Dec 10, 2021
Cite this dataset
No linked publication found — please cite the data source.
License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB