Visium

Human prostate gland

MEND139

silver Interactive viewer H&E prostatic acinar adenocarcinoma ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'MEND139_full_image': DataTree[cyx] (3, 24258, 24000), (3, 12129, 12000), (3, 6064, 6000), (3, 3032, 3000)
├── Shapes
│     └── 'MEND139_spots': GeoDataFrame shape: (3749, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (3749, 33538)
with coordinate systems:
    ▸ 'global', with elements:
        MEND139_full_image (Images), MEND139_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("Sqy7y6B7y6b3d4Ze0000")
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("Sqy7y6B7y6b3d4Ze")   # 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 Sqy7y6B7y6b3d4Ze0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Sqy7y6B7y6b3d4Ze

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Sqy7y6B7y6b3d4Ze

Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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Part of collection

Spatially resolved clonal copy number alterations in benign and malignant tissueJus→

23 datasets · replicates

Metadata

Technology: Visium
Organism: human
Tissue: prostate gland
Condition: prostatic acinar adenocarcinoma
Modality: RNA
Observations (spots): 3,749
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 24,000 × 24,258 px
mpp: 0.342 µm/px
Size: 1.4 GB
Sample ID: MEND139
License: CC BY-NC-SA 4.0 NonCommercial
Published: Mar 25, 2024

Cite this dataset

doi.org/10.1038/s41586-022-05023-2 ↗

BibTeX

@article{Erickson_2022,
  title = {Spatially resolved clonal copy number alterations in benign and malignant tissue},
  volume = {608},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-022-05023-2},
  DOI = {10.1038/s41586-022-05023-2},
  number = {7922},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Erickson, Andrew and He, Mengxiao and Berglund, Emelie and Marklund, Maja and Mirzazadeh, Reza and Schultz, Niklas and Kvastad, Linda and Andersson, Alma and Bergenstråhle, Ludvig and Bergenstråhle, Joseph and Larsson, Ludvig and Alonso Galicia, Leire and Shamikh, Alia and Basmaci, Elisa and Díaz De Ståhl, Teresita and Rajakumar, Timothy and Doultsinos, Dimitrios and Thrane, Kim and Ji, Andrew L. and Khavari, Paul A. and Tarish, Firaz and Tanoglidi, Anna and Maaskola, Jonas and Colling, Richard and Mirtti, Tuomas and Hamdy, Freddie C. and Woodcock, Dan J. and Helleday, Thomas and Mills, Ian G. and Lamb, Alastair D. and Lundeberg, Joakim},
  year = {2022},
  month = Aug,
  pages = {360–367}
}

Source: nature.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB