Visium
Mouse brain
GSM5026148
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM5026148_S2_hires_image': DataArray[cyx] (3, 2000, 1865)
│ └── 'GSM5026148_S2_lowres_image': DataArray[cyx] (3, 600, 560)
├── Shapes
│ └── 'GSM5026148_S2': GeoDataFrame shape: (2157, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2157, 32285)
with coordinate systems:
▸ 'GSM5026148_S2', with elements:
GSM5026148_S2_hires_image (Images), GSM5026148_S2_lowres_image (Images), GSM5026148_S2 (Shapes)
▸ 'GSM5026148_S2_downscaled_hires', with elements:
GSM5026148_S2_hires_image (Images), GSM5026148_S2 (Shapes)
▸ 'GSM5026148_S2_downscaled_lowres', with elements:
GSM5026148_S2_lowres_image (Images), GSM5026148_S2 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("1aKQZN54OskFrGyw0000")
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("1aKQZN54OskFrGyw") # 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 1aKQZN54OskFrGyw0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/1aKQZN54OskFrGyw
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1aKQZN54OskFrGywLicense: NCBI GEO policy
Part of collection
Neuroinflammatory astrocyte subtypes in the mouse brain [Visium]→ 6 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,157
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,865 × 2,000 px
- mpp
- 3.532 µm/px
- Size
- 54.0 MB
- Sample ID
- GSM5026148
- License
- NCBI GEO policy
- Published
- Jun 3, 2021
Cite this dataset
doi.org/10.1038/s41593-021-00905-6 ↗ BibTeX
@article{Hasel_2021,
title = {Neuroinflammatory astrocyte subtypes in the mouse brain},
volume = {24},
ISSN = {1546-1726},
url = {http://dx.doi.org/10.1038/s41593-021-00905-6},
DOI = {10.1038/s41593-021-00905-6},
number = {10},
journal = {Nature Neuroscience},
publisher = {Springer Science and Business Media LLC},
author = {Hasel, Philip and Rose, Indigo V. L. and Sadick, Jessica S. and Kim, Rachel D. and Liddelow, Shane A.},
year = {2021},
month = Aug,
pages = {1475–1487}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB