Visium
Human lymph node
GSM8633892
bronze Interactive viewer H&E head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8633892_21_00758_LI_SING_hires_image': DataArray[cyx] (3, 2000, 1973)
│ └── 'GSM8633892_21_00758_LI_SING_lowres_image': DataArray[cyx] (3, 600, 592)
├── Shapes
│ └── 'GSM8633892_21_00758_LI_SING': GeoDataFrame shape: (1579, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1579, 36601)
with coordinate systems:
▸ 'GSM8633892_21_00758_LI_SING', with elements:
GSM8633892_21_00758_LI_SING_hires_image (Images), GSM8633892_21_00758_LI_SING_lowres_image (Images), GSM8633892_21_00758_LI_SING (Shapes)
▸ 'GSM8633892_21_00758_LI_SING_downscaled_hires', with elements:
GSM8633892_21_00758_LI_SING_hires_image (Images), GSM8633892_21_00758_LI_SING (Shapes)
▸ 'GSM8633892_21_00758_LI_SING_downscaled_lowres', with elements:
GSM8633892_21_00758_LI_SING_lowres_image (Images), GSM8633892_21_00758_LI_SING (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("FOVxWXpoaMHgdyYL0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("FOVxWXpoaMHgdyYL") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download FOVxWXpoaMHgdyYL0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/FOVxWXpoaMHgdyYL
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid FOVxWXpoaMHgdyYLLicense: NCBI GEO policy
Part of collection
Deciphering head and neck cancer microenvironment: Single‐cell and spatial transcriptomics reveals human papillomavirus‐associated differences→ 5 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lymph node
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations (spots)
- 1,579
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,973 × 2,000 px
- mpp
- 3.294 µm/px
- Size
- 36.2 MB
- Sample ID
- GSM8633892
- License
- NCBI GEO policy
- Published
- Nov 20, 2024
Cite this dataset
doi.org/10.1002/jmv.29386 ↗ BibTeX
@article{Lee_2024,
title = {Deciphering head and neck cancer microenvironment: Single‐cell and spatial transcriptomics reveals human papillomavirus‐associated differences},
volume = {96},
ISSN = {1096-9071},
url = {http://dx.doi.org/10.1002/jmv.29386},
DOI = {10.1002/jmv.29386},
number = {1},
journal = {Journal of Medical Virology},
publisher = {Wiley},
author = {Lee, Hansong and Park, Sohee and Yun, Ju Hyun and Seo, Chorong and Ahn, Ji Mi and Cha, Hyun‐Young and Shin, Yoo Seob and Park, Hae Ryoun and Lee, Dongjun and Roh, Jin and Heo, Hye Jin and Baek, Seung Eun and Kim, Eun Kyoung and Lee, Hae Seul and Kim, Chul‐Ho and Kim, Yun Hak and Jang, Jeon Yeob},
year = {2024},
month = Jan
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB