CosMx SMI
Human liver
Nanostring CosMx (HCC tumour LC36T, Run5275) [figshare 23972991]
bronze Interactive viewer hepatocellular carcinoma Provisional
print(sdata)
SpatialData object
├── Points
│ └── 'points': DataFrame with shape: (96078068, 11) (2D points)
├── Shapes
│ ├── 'cells_polygons': GeoDataFrame shape: (71528, 9) (2D shapes)
│ ├── 'cells_polygons_for_vitessce': GeoDataFrame shape: (71528, 2) (2D shapes)
│ └── 'fov_boxes': GeoDataFrame shape: (23, 2) (2D shapes)
└── Tables
└── 'table': AnnData (71528, 979)
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("MnfwoSV4aqNYzxa70000")
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("MnfwoSV4aqNYzxa7") # 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 MnfwoSV4aqNYzxa70000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/MnfwoSV4aqNYzxa7
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid MnfwoSV4aqNYzxa7License: CC BY 4.0
Metadata
- Technology
- CosMx SMI
- Vendor
- Bruker
- Organism
- human
- Tissue
- liver
- Condition
- hepatocellular carcinoma
- Modality
- RNA
- Observations (cells)
- 71,528
- Transcripts
- 26,501,556
- Target genes
- 960
- Tier
- bronze
- Size
- 993 MB
- Sample ID
- 23972991:Run5275_LC36_T
- License
- CC BY 4.0
- Published
- Apr 12, 2024
Cite this dataset
doi.org/10.6084/m9.figshare.23972991.v2 ↗ BibTeX
@article{figshare:23972991,
doi = {10.6084/m9.figshare.23972991.v2},
title = {Nanostring CosMx (HCC tumour LC36T, Run5275) [figshare 23972991]},
year = {2024}
}Source: figshare.com ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB