spatial transcriptomics
Human skin of body
NCBI760
silver Interactive viewer H&E skin squamous cell carcinoma ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI760_full_image': DataTree[cyx] (3, 15872, 15872), (3, 7936, 7936), (3, 3968, 3968), (3, 1984, 1984)
├── Shapes
│ └── 'NCBI760_spots': GeoDataFrame shape: (621, 2) (2D shapes)
└── Tables
└── 'table': AnnData (621, 15684)
with coordinate systems:
▸ 'global', with elements:
NCBI760_full_image (Images), NCBI760_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("oi8oxLDwPQUJJ4Yj0000")
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("oi8oxLDwPQUJJ4Yj") # 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 oi8oxLDwPQUJJ4Yj0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/oi8oxLDwPQUJJ4Yj
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid oi8oxLDwPQUJJ4YjLicense: CC BY-NC-SA 4.0 (noncommercial)
Part of collection
Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [ST]→ 16 datasets · replicates
Metadata
- Technology
- spatial transcriptomics
- Organism
- human
- Tissue
- skin of body
- Condition
- skin squamous cell carcinoma
- Modality
- RNA
- Observations (spots)
- 621
- Tier
- silver
- Chemistry
- ST 2k
- Magnification
- 20x
- Resolution
- 15,872 × 15,872 px
- mpp
- 0.366 µm/px
- Size
- 203 MB
- Sample ID
- NCBI760
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Jun 22, 2020
Cite this dataset
doi.org/10.1016/j.cell.2020.05.039 ↗ BibTeX
@article{Ji_2020,
title = {Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma},
volume = {182},
ISSN = {0092-8674},
url = {http://dx.doi.org/10.1016/j.cell.2020.05.039},
DOI = {10.1016/j.cell.2020.05.039},
number = {2},
journal = {Cell},
publisher = {Elsevier BV},
author = {Ji, Andrew L. and Rubin, Adam J. and Thrane, Kim and Jiang, Sizun and Reynolds, David L. and Meyers, Robin M. and Guo, Margaret G. and George, Benson M. and Mollbrink, Annelie and Bergenstråhle, Joseph and Larsson, Ludvig and Bai, Yunhao and Zhu, Bokai and Bhaduri, Aparna and Meyers, Jordan M. and Rovira-Clavé, Xavier and Hollmig, S. Tyler and Aasi, Sumaira Z. and Nolan, Garry P. and Lundeberg, Joakim and Khavari, Paul A.},
year = {2020},
month = July,
pages = {497–514.e22}
}Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB