CosMx SMI

Human unknown

GSE277782:Run5961_PDAC_Slide1

bronze Interactive viewer pancreatic ductal adenocarcinoma Provisional

CosMx SMI

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Points
│     └── 'points': DataFrame with shape: (30616836, 11) (2D points)
├── Shapes
│     ├── 'cells_polygons': GeoDataFrame shape: (35385, 9) (2D shapes)
│     ├── 'cells_polygons_for_vitessce': GeoDataFrame shape: (35385, 2) (2D shapes)
│     └── 'fov_boxes': GeoDataFrame shape: (45, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (35385, 1010)
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)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("dqnjrKqHhQuSdQD00000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("dqnjrKqHhQuSdQD0")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download dqnjrKqHhQuSdQD00000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/dqnjrKqHhQuSdQD0

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid dqnjrKqHhQuSdQD0

Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

geo-gse277782→

2 datasets · publication

Metadata

Technology: CosMx SMI
Vendor: Bruker
Organism: human
Tissue: unknown
Condition: pancreatic ductal adenocarcinoma
Modality: RNA
Observations (cells): 35,385
Transcripts: 10,205,612
Tier: bronze
Size: 389 MB
Sample ID: GSE277782:Run5961_PDAC_Slide1
License: NCBI GEO policy
Published: Feb 21, 2025

Cite this dataset

No linked publication found — please cite the data source: NCBI GEO ↗.

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB