Visium

Mouse eye

NCBI435

silver Interactive viewer H&E ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI435_full_image': DataTree[cyx] (3, 10828, 10612), (3, 5414, 5306), (3, 2707, 2653), (3, 1353, 1326)
├── Shapes
│     └── 'NCBI435_spots': GeoDataFrame shape: (1106, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1106, 32285)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI435_full_image (Images), NCBI435_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("TRp86aypNzNgq3jv0000")
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("TRp86aypNzNgq3jv")   # 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 TRp86aypNzNgq3jv0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/TRp86aypNzNgq3jv

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid TRp86aypNzNgq3jv

Install (Python 3.12+) Docs →

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

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

Part of collection

Visium spatial transcriptomics analysis of lacrimal gland during chronic inflammation progression.→

4 datasets · comparison

Metadata

Technology: Visium
Organism: mouse
Tissue: eye
Modality: RNA
Observations (spots): 1,106
Tier: silver
Chemistry: Visium v1
Resolution: 10,612 × 10,828 px
mpp: 0.752 µm/px
Size: 227 MB
Sample ID: NCBI435
License: CC BY-NC-SA 4.0 NonCommercial
Published: Sep 23, 2022

Cite this dataset

doi.org/10.3389/fimmu.2022.1011125 ↗

BibTeX

@article{Mauduit_2022,
  title = {Spatial transcriptomics of the lacrimal gland features macrophage activity and epithelium metabolism as key alterations during chronic inflammation},
  volume = {13},
  ISSN = {1664-3224},
  url = {http://dx.doi.org/10.3389/fimmu.2022.1011125},
  DOI = {10.3389/fimmu.2022.1011125},
  journal = {Frontiers in Immunology},
  publisher = {Frontiers Media SA},
  author = {Mauduit, Olivier and Delcroix, Vanessa and Umazume, Takeshi and de Paiva, Cintia S. and Dartt, Darlene A. and Makarenkova, Helen P.},
  year = {2022},
  month = Oct
}

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