Visium

Human eye

NCBI771

silver Interactive viewer H&E adenoid cystic carcinoma ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI771_full_image': DataTree[cyx] (3, 9011, 10458), (3, 4505, 5229), (3, 2252, 2614), (3, 1126, 1307)
├── Shapes
│     └── 'NCBI771_spots': GeoDataFrame shape: (3584, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (3584, 17943)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI771_full_image (Images), NCBI771_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("Or0OhPZsZhhyJpTP0000")
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("Or0OhPZsZhhyJpTP")   # 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 Or0OhPZsZhhyJpTP0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Or0OhPZsZhhyJpTP

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Or0OhPZsZhhyJpTP

Install (Python 3.12+) Docs →

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

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Metadata

Technology: Visium
Organism: human
Tissue: eye
Condition: adenoid cystic carcinoma
Modality: RNA
Observations (spots): 3,584
Tier: silver
Chemistry: Visium v1
Resolution: 10,458 × 9,011 px
mpp: 1.010 µm/px
Size: 163 MB
Sample ID: NCBI771
License: CC BY-NC-SA 4.0 NonCommercial
Published: Jul 5, 2023

Cite this dataset

doi.org/10.3390/cancers15123211 ↗

BibTeX

@article{Moeyersoms_2023,
  title = {Spatial Transcriptomics Identifies Expression Signatures Specific to Lacrimal Gland Adenoid Cystic Carcinoma Cells},
  volume = {15},
  ISSN = {2072-6694},
  url = {http://dx.doi.org/10.3390/cancers15123211},
  DOI = {10.3390/cancers15123211},
  number = {12},
  journal = {Cancers},
  publisher = {MDPI AG},
  author = {Moeyersoms, Acadia H. M. and Gallo, Ryan A. and Zhang, Michelle G. and Stathias, Vasileios and Maeng, Michelle M. and Owens, Dawn and Abou Khzam, Rayan and Sayegh, Yoseph and Maza, Cynthia and Dubovy, Sander R. and Tse, David T. and Pelaez, Daniel},
  year = {2023},
  month = June,
  pages = {3211}
}

Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB