Visium

Human uterine cervix

NCBI4

silver Interactive viewer H&E human papilloma virus infection ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI4_full_image': DataTree[cyx] (3, 9681, 9920), (3, 4840, 4960), (3, 2420, 2480), (3, 1210, 1240)
├── Shapes
│     └── 'NCBI4_spots': GeoDataFrame shape: (1054, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1054, 20615)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI4_full_image (Images), NCBI4_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("U5VYqoc0wA97cp3g0000")
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("U5VYqoc0wA97cp3g")   # 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 U5VYqoc0wA97cp3g0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/U5VYqoc0wA97cp3g

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid U5VYqoc0wA97cp3g

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

Spatiotemporally Deciphering the Unknown Role of Persistent HPV Infection in Precancer to Cervical Cancer Progression: Integrating Single-Cell RNA-Sequencing Landscape and Spatial Transcriptomics Atlas [Spatial Transcriptomics]→

4 datasets · comparison

Metadata

Technology: Visium
Organism: human
Tissue: uterine cervix
Condition: human papilloma virus infection
Modality: RNA
Observations (spots): 1,054
Tier: silver
Chemistry: Visium v1
Resolution: 9,920 × 9,681 px
mpp: 0.882 µm/px
Size: 145 MB
Sample ID: NCBI4
License: CC BY-NC-SA 4.0 NonCommercial
Published: Apr 2, 2023

Cite this dataset

doi.org/10.1002/ctm2.1219 ↗

BibTeX

@article{Guo_2023,
  title = {Spatiotemporally deciphering the mysterious mechanism of persistent HPV‐induced malignant transition and immune remodelling from HPV‐infected normal cervix, precancer to cervical cancer: Integrating single‐cell RNA‐sequencing and spatial transcriptome},
  volume = {13},
  ISSN = {2001-1326},
  url = {http://dx.doi.org/10.1002/ctm2.1219},
  DOI = {10.1002/ctm2.1219},
  number = {3},
  journal = {Clinical and Translational Medicine},
  publisher = {Wiley},
  author = {Guo, Chenyan and Qu, Xinyu and Tang, Xiaoyan and Song, Yu and Wang, Jue and Hua, Keqin and Qiu, Junjun},
  year = {2023},
  month = Mar
}

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