CosMx SMI
Human skin of body
11108209:Run5469_S1
bronze Interactive viewer melanoma Provisional
print(sdata)
SpatialData object
├── Points
│ └── 'points': DataFrame with shape: (24326670, 11) (2D points)
├── Shapes
│ ├── 'cells_polygons': GeoDataFrame shape: (67576, 9) (2D shapes)
│ ├── 'cells_polygons_for_vitessce': GeoDataFrame shape: (67576, 2) (2D shapes)
│ └── 'fov_boxes': GeoDataFrame shape: (25, 2) (2D shapes)
└── Tables
└── 'table': AnnData (67576, 987)
with coordinate systems:
▸ 'global', with elements:
points (Points), cells_polygons (Shapes), cells_polygons_for_vitessce (Shapes), fov_boxes (Shapes)
▸ 'microns', with elements:
points (Points), cells_polygons (Shapes), cells_polygons_for_vitessce (Shapes), fov_boxes (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("lYqsBFejK75ipZkf0000")
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("lYqsBFejK75ipZkf") # 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 lYqsBFejK75ipZkf0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/lYqsBFejK75ipZkf
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid lYqsBFejK75ipZkfLicense: CC0 1.0
Metadata
- Technology
- CosMx SMI
- Vendor
- Bruker
- Organism
- human
- Tissue
- skin of body
- Condition
- melanoma
- Modality
- RNA
- Observations (cells)
- 67,576
- Transcripts
- 24,326,670
- Tier
- bronze
- Size
- 876 MB
- Sample ID
- 11108209:Run5469_S1
- License
- CC0 1.0
- Published
- May 3, 2024
Cite this dataset
No linked publication found — please cite the data source: zenodo.org ↗.
Source: zenodo.org ↗ · License: CC0 1.0 ↗ · Reprocessed to SpatialData by SpatialData-DB