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Visium

Human eye

NCBI771

silver Interactive viewer H&E adenoid cystic carcinoma ✓ Verified publication
Human eye preview
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)
Load in Python 
import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Or0OhPZsZhhyJpTP")   # 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
Load from the CLI 
# one-shot: 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
Load with the Python client 
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["Or0OhPZsZhhyJpTP0000"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

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Metadata

Technology
Visium
Organism
human
Tissue
eye
Condition
adenoid cystic carcinoma
Modality
RNA
Observations
3,584
Tier
silver
Chemistry
Visium v1
Resolution
10,458 × 9,011 px
mpp
1.010 µm/px
Size
155 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