Visium
Human craniocervical region
GSM5494480
bronze Interactive viewer H&E head and neck squamous cell carcinoma Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM5494480_P210325T3_hires_image': DataArray[cyx] (3, 2000, 1946)
├── Shapes
│ └── 'GSM5494480_P210325T3': GeoDataFrame shape: (1853, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1853, 36601)
with coordinate systems:
▸ 'GSM5494480_P210325T3', with elements:
GSM5494480_P210325T3_hires_image (Images), GSM5494480_P210325T3 (Shapes)
▸ 'GSM5494480_P210325T3_downscaled_hires', with elements:
GSM5494480_P210325T3_hires_image (Images), GSM5494480_P210325T3 (Shapes)
▸ 'GSM5494480_P210325T3_downscaled_lowres', with elements:
GSM5494480_P210325T3 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("XMPlJQ3XNx5sBcXR0000")
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("XMPlJQ3XNx5sBcXR") # 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 XMPlJQ3XNx5sBcXR0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/XMPlJQ3XNx5sBcXR
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid XMPlJQ3XNx5sBcXRLicense: NCBI GEO policy
Part of collection
Visium Analysis of head and neck squamous carcinoma (HNSCC) spatial transcriptome evolution→ 8 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- craniocervical region
- Condition
- head and neck squamous cell carcinoma
- Modality
- RNA
- Observations (spots)
- 1,853
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 1,946 × 2,000 px
- mpp
- 3.881 µm/px
- Size
- 14.4 MB
- Sample ID
- GSM5494480
- License
- NCBI GEO policy
- Published
- Aug 29, 2022
Cite this dataset
doi.org/10.1136/jitc-2022-004832 ↗ BibTeX
@article{Cheng_2022,
title = {Snail-regulated exosomal microRNA-21 suppresses NLRP3 inflammasome activity to enhance cisplatin resistance},
volume = {10},
ISSN = {2051-1426},
url = {http://dx.doi.org/10.1136/jitc-2022-004832},
DOI = {10.1136/jitc-2022-004832},
number = {8},
journal = {Journal for ImmunoTherapy of Cancer},
publisher = {BMJ},
author = {Cheng, Han-Ying and Hsieh, Chia-Hsin and Lin, Po-Han and Chen, Yu-Tung and Hsu, Dennis Shin-Shian and Tai, Shyh-Kuan and Chu, Pen-Yuan and Yang, Muh-Hwa},
year = {2022},
month = Aug,
pages = {e004832}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB