Visium

Mouse liver

NCBI627

silver Interactive viewer H&E hepatoblastoma ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI627_full_image': DataTree[cyx] (3, 10000, 9897), (3, 5000, 4948), (3, 2500, 2474), (3, 1250, 1237)
├── Shapes
│     └── 'NCBI627_spots': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4992, 31053)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI627_full_image (Images), NCBI627_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("qtGEj64YmBUyhjt90000")
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("qtGEj64YmBUyhjt9")   # 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 qtGEj64YmBUyhjt90000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/qtGEj64YmBUyhjt9

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid qtGEj64YmBUyhjt9

Install (Python 3.12+) Docs →

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

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Part of collection

mousemodel_Heptablastoma spatial transcriptomics→

10 datasets · publication

Metadata

Technology: Visium
Organism: mouse
Tissue: liver
Condition: hepatoblastoma
Modality: RNA
Observations (spots): 4,992
Tier: silver
Chemistry: Visium v1
Resolution: 9,897 × 10,000 px
mpp: 0.891 µm/px
Size: 244 MB
Sample ID: NCBI627
License: CC BY-NC-SA 4.0 NonCommercial
Published: Jun 9, 2023

Cite this dataset

doi.org/10.1038/s41467-023-39717-6 ↗

BibTeX

@article{Fang_2023,
  title = {Genome-wide mapping of cancer dependency genes and genetic modifiers of chemotherapy in high-risk hepatoblastoma},
  volume = {14},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-023-39717-6},
  DOI = {10.1038/s41467-023-39717-6},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Fang, Jie and Singh, Shivendra and Cheng, Changde and Natarajan, Sivaraman and Sheppard, Heather and Abu-Zaid, Ahmed and Durbin, Adam D. and Lee, Ha Won and Wu, Qiong and Steele, Jacob and Connelly, Jon P. and Jin, Hongjian and Chen, Wenan and Fan, Yiping and Pruett-Miller, Shondra M. and Rehg, Jerold E. and Koo, Selene C. and Santiago, Teresa and Emmons, Joseph and Cairo, Stefano and Wang, Ruoning and Glazer, Evan S. and Murphy, Andrew J. and Chen, Taosheng and Davidoff, Andrew M. and Armengol, Carolina and Easton, John and Chen, Xiang and Yang, Jun},
  year = {2023},
  month = July
}

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