Visium

Human breast

GSM8789207

silver Interactive viewer H&E breast neoplasm ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8789207_HCC22-088-P3-S1_A_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│     ├── 'GSM8789207_HCC22-088-P3-S1_A_hires_image': DataArray[cyx] (3, 1961, 2000)
│     └── 'GSM8789207_HCC22-088-P3-S1_A_lowres_image': DataArray[cyx] (3, 588, 600)
├── Shapes
│     └── 'GSM8789207_HCC22-088-P3-S1_A': GeoDataFrame shape: (423, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (423, 18085)
with coordinate systems:
    ▸ 'GSM8789207_HCC22-088-P3-S1_A', with elements:
        GSM8789207_HCC22-088-P3-S1_A_full_image (Images), GSM8789207_HCC22-088-P3-S1_A_hires_image (Images), GSM8789207_HCC22-088-P3-S1_A_lowres_image (Images), GSM8789207_HCC22-088-P3-S1_A (Shapes)
    ▸ 'GSM8789207_HCC22-088-P3-S1_A_downscaled_hires', with elements:
        GSM8789207_HCC22-088-P3-S1_A_hires_image (Images), GSM8789207_HCC22-088-P3-S1_A (Shapes)
    ▸ 'GSM8789207_HCC22-088-P3-S1_A_downscaled_lowres', with elements:
        GSM8789207_HCC22-088-P3-S1_A_lowres_image (Images), GSM8789207_HCC22-088-P3-S1_A (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("WU9PlyJMQv7JrB2S0000")
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("WU9PlyJMQv7JrB2S")   # 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 WU9PlyJMQv7JrB2S0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/WU9PlyJMQv7JrB2S

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid WU9PlyJMQv7JrB2S

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

CITEgeist: Cellular Indexing of Transcriptomes and Epitopes for Guided Exploration of Intrinsic Spatial Trends→

14 datasets · comparison

Metadata

Technology: Visium
Organism: human
Tissue: breast
Condition: breast neoplasm
Modality: RNA
Observations (spots): 423
Tier: silver
Chemistry: Visium CytAssist v2
Magnification: 20x
Resolution: 3,000 × 3,000 px
mpp: 0.397 µm/px
Size: 31.0 MB
Sample ID: GSM8789207
License: NCBI GEO policy
Published: Mar 19, 2026

Cite this dataset

doi.org/10.1158/1078-0432.ccr-25-4079 ↗

BibTeX

@article{Carleton_2026,
  title = {Use of ctDNA in Older Women with ER+ Breast Cancer to Facilitate Surgical De-escalation: A Prospective, Hybrid-Decentralized Trial with Correlative Studies},
  volume = {32},
  ISSN = {1557-3265},
  url = {http://dx.doi.org/10.1158/1078-0432.ccr-25-4079},
  DOI = {10.1158/1078-0432.ccr-25-4079},
  number = {14},
  journal = {Clinical Cancer Research},
  publisher = {American Association for Cancer Research (AACR)},
  author = {Carleton, Neil and Chang, Alexander C. and Chen, Fangyuan and Puhalla, Shannon L. and Foldi, Julia and Waltermire, Hunter and Tin, Antony and Cowher, Michael S. and Lupinacci, Kristin and Diego, Emilia J. and Sabih, Quratulain and Johnson, Ronald R. and Malhotra, Monica and Laubenthal, Amanda and Gorantla, Vikram and Balic, Marija and Bhargava, Rohit and Joy, Marion and Freeman, Tanner and Bridges, Catherine and Kalashnikova, Ekaterina and Rodriguez, Angel and Liu, Minetta C. and Oesterreich, Steffi and Lee, Adrian V. and McAuliffe, Priscilla F.},
  year = {2026},
  month = Mar,
  pages = {2957–2967}
}

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