Visium
Mouse mediastinal lymph node
GSM7836927
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7836927_LND5-1_hires_image': DataArray[cyx] (3, 1961, 2000)
│ └── 'GSM7836927_LND5-1_lowres_image': DataArray[cyx] (3, 588, 600)
├── Shapes
│ └── 'GSM7836927_LND5-1': GeoDataFrame shape: (621, 2) (2D shapes)
└── Tables
└── 'table': AnnData (621, 32285)
with coordinate systems:
▸ 'GSM7836927_LND5-1', with elements:
GSM7836927_LND5-1_hires_image (Images), GSM7836927_LND5-1_lowres_image (Images), GSM7836927_LND5-1 (Shapes)
▸ 'GSM7836927_LND5-1_downscaled_hires', with elements:
GSM7836927_LND5-1_hires_image (Images), GSM7836927_LND5-1 (Shapes)
▸ 'GSM7836927_LND5-1_downscaled_lowres', with elements:
GSM7836927_LND5-1_lowres_image (Images), GSM7836927_LND5-1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("7WHUXwyPwsXZQOop0000")
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("7WHUXwyPwsXZQOop") # 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 7WHUXwyPwsXZQOop0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/7WHUXwyPwsXZQOop
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7WHUXwyPwsXZQOopLicense: NCBI GEO policy
Part of collection
Spatial microniches of IL-2 synergize with IL-10 to drive lung migratory Th2 cells in response to inhaled allergen [Spatial transcriptomics]→ 4 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- mediastinal lymph node
- Modality
- RNA
- Observations (spots)
- 621
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,961 px
- mpp
- 3.762 µm/px
- Size
- 7.7 MB
- Sample ID
- GSM7836927
- License
- NCBI GEO policy
- Published
- Feb 20, 2024
Cite this dataset
doi.org/10.1038/s41592-024-02175-z ↗ BibTeX
@article{Rahimikollu_2024,
title = {SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains},
volume = {21},
ISSN = {1548-7105},
url = {http://dx.doi.org/10.1038/s41592-024-02175-z},
DOI = {10.1038/s41592-024-02175-z},
number = {5},
journal = {Nature Methods},
publisher = {Springer Science and Business Media LLC},
author = {Rahimikollu, Javad and Xiao, Hanxi and Rosengart, AnnaElaine and Rosen, Aaron B. I. and Tabib, Tracy and Zdinak, Paul M. and He, Kun and Bing, Xin and Bunea, Florentina and Wegkamp, Marten and Poholek, Amanda C. and Joglekar, Alok V. and Lafyatis, Robert A. and Das, Jishnu},
year = {2024},
month = Feb,
pages = {835–845}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB