Slide-seq
Human axilla
HTAPP-812-SMP-8239 Slide-seq (Slide-seqV2; HTAN/HTAPP Broad - Spatio-molecular dissection of the breast cancer metastatic microenvironment)
bronze Interactive viewer breast cancer Provisional
print(sdata)
SpatialData object
├── Shapes
│ └── 'cells': GeoDataFrame shape: (10957, 2) (2D shapes)
└── Tables
└── 'table': AnnData (10957, 15507)
with coordinate systems:
▸ 'global', with elements:
cells (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("nlM6CeK02rHtQhYu0000")
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("nlM6CeK02rHtQhYu") # 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 nlM6CeK02rHtQhYu0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/nlM6CeK02rHtQhYu
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid nlM6CeK02rHtQhYuLicense: CC BY 4.0
Metadata
- Technology
- Slide-seq
- Vendor
- Academic
- Organism
- human
- Tissue
- axilla
- Condition
- breast cancer
- Modality
- RNA
- Observations (spots)
- 10,957
- Tier
- bronze
- Size
- 10.1 MB
- Sample ID
- f12ab0e6-383c-4362-b1c6-922de09ccbc9
- License
- CC BY 4.0
- Published
- Oct 2, 2024
Cite this dataset
doi.org/10.1038/s41591-024-03215-z ↗ BibTeX
@article{cellxgene:a96133de-e951-4e2d-ace6-59db8b3bfb1d,
doi = {10.1038/s41591-024-03215-z},
title = {HTAPP-853-SMP-4381 Slide-seq (Slide-seqV2; HTAN/HTAPP Broad - Spatio-molecular dissection of the breast cancer metastatic microenvironment)},
year = {2024}
}Source: cellxgene.cziscience.com ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB