CosMx SMI

Human prostate gland

GSM8649315

bronze Interactive viewer prostate cancer Provisional

CosMx SMI

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Points
│     └── 'points': DataFrame with shape: (18532453, 11) (2D points)
├── Shapes
│     ├── 'cells_polygons': GeoDataFrame shape: (140336, 9) (2D shapes)
│     ├── 'cells_polygons_for_vitessce': GeoDataFrame shape: (140336, 2) (2D shapes)
│     └── 'fov_boxes': GeoDataFrame shape: (25, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (140336, 980)
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("9yt1RFMqoIc6JHEy0000")
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("9yt1RFMqoIc6JHEy")   # 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 9yt1RFMqoIc6JHEy0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/9yt1RFMqoIc6JHEy

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 9yt1RFMqoIc6JHEy

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

geo-gse282721→

1 datasets · publication

Metadata

Technology: CosMx SMI
Vendor: Bruker
Organism: human
Tissue: prostate gland
Condition: prostate cancer
Modality: RNA
Observations (cells): 140,336
Transcripts: 18,532,453
Tier: bronze
Size: 717 MB
Sample ID: GSM8649315
License: NCBI GEO policy
Published: Feb 21, 2026

Cite this dataset

doi.org/10.1038/s41467-026-71121-8 ↗

BibTeX

@article{Brea_2026,
  title = {FOXA1 loss drives basal/squamous de-differentiation of prostate cancer and induces an immunosuppressive tumor microenvironment},
  volume = {17},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-026-71121-8},
  DOI = {10.1038/s41467-026-71121-8},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Brea, Lourdes and Shi, Hongshun and Keo, Viriya and Huang, Jing and Peng, Liu and Chu, Qi and Xie, Wanqing and Xie, Yinghua and Senthil, Sambhavi and Breneman, Matthew T. and Fan, Jie and Xie, Ping and Lu, Xiaodong and Degraff, David J. and Abdulkadir, Sarki A. and Yang, Ximing and Kosoff, David and Zhao, Jonathan C. and Zhang, Bin and Hu, Jian and Yu, Jindan},
  year = {2026},
  month = Mar
}

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