Visium
Mouse brain
GSM8472672
bronze Interactive viewer H&E Venezuelan equine encephalitis Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8472672_I_hires_image': DataArray[cyx] (3, 2000, 2000)
│ └── 'GSM8472672_I_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM8472672_I': GeoDataFrame shape: (4992, 2) (2D shapes)
└── Tables
└── 'table': AnnData (4992, 32589)
with coordinate systems:
▸ 'GSM8472672_I', with elements:
GSM8472672_I_hires_image (Images), GSM8472672_I_lowres_image (Images), GSM8472672_I (Shapes)
▸ 'GSM8472672_I_downscaled_hires', with elements:
GSM8472672_I_hires_image (Images), GSM8472672_I (Shapes)
▸ 'GSM8472672_I_downscaled_lowres', with elements:
GSM8472672_I_lowres_image (Images), GSM8472672_I (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("J1XnSOye3fVQDJ6S0000")
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("J1XnSOye3fVQDJ6S") # 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 J1XnSOye3fVQDJ6S0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/J1XnSOye3fVQDJ6S
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid J1XnSOye3fVQDJ6SLicense: NCBI GEO policy
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Condition
- Venezuelan equine encephalitis
- Modality
- RNA
- Observations (spots)
- 4,992
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 2,000 px
- mpp
- 5.488 µm/px
- Size
- 51.7 MB
- Sample ID
- GSM8472672
- License
- NCBI GEO policy
- Published
- Dec 9, 2024
Cite this dataset
doi.org/10.3389/fimmu.2024.1497839 ↗ BibTeX
@article{Rangel_2024,
title = {Single-cell and spatiotemporal transcriptomic profiling of brain immune infiltration following Venezuelan equine encephalitis virus infection},
volume = {15},
ISSN = {1664-3224},
url = {http://dx.doi.org/10.3389/fimmu.2024.1497839},
DOI = {10.3389/fimmu.2024.1497839},
journal = {Frontiers in Immunology},
publisher = {Frontiers Media SA},
author = {Rangel, Margarita V. and Sebastian, Aimy and Leon, Nicole F. and Phillips, Ashlee M. and Gorman, Bria M. and Hum, Nicholas R. and Weilhammer, Dina R.},
year = {2024},
month = Dec
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB