Slide-seq
Human lymph node
Normal Lymph Node Puck_201014_06 (Slide-seqV2; Spatially mapping T cell receptors and transcriptomes)
bronze Interactive viewer Provisional
print(sdata)
SpatialData object
├── Shapes
│ └── 'cells': GeoDataFrame shape: (26027, 2) (2D shapes)
└── Tables
└── 'table': AnnData (26027, 23444)
with coordinate systems:
▸ 'global', with elements:
cells (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("pD48PsEqKzlgL5gA0000")
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("pD48PsEqKzlgL5gA") # 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 pD48PsEqKzlgL5gA0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/pD48PsEqKzlgL5gA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid pD48PsEqKzlgL5gALicense: CC BY 4.0
Metadata
- Technology
- Slide-seq
- Vendor
- Academic
- Organism
- human
- Tissue
- lymph node
- Modality
- RNA
- Observations (spots)
- 26,027
- Tier
- bronze
- Size
- 33.7 MB
- Sample ID
- fb5b437f-69b8-47ee-82ed-b5e784193d64
- License
- CC BY 4.0
- Published
- Sep 29, 2023
Cite this dataset
doi.org/10.1016/j.immuni.2022.09.002 ↗ BibTeX
@article{cellxgene:02b01703-bf1b-48de-b99a-23bef8cccc81,
doi = {10.1016/j.immuni.2022.09.002},
title = {Cutaneous melanoma, lymph node metastasis Puck_220408_07 (Slide-seqV2; Spatially mapping T cell receptors and transcriptomes)},
year = {2022}
}Source: cellxgene.cziscience.com ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB