Visium
Mouse brain
GSM7020543
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM7020543_A2_OB_virgin_hires_image': DataArray[cyx] (3, 1753, 2000)
├── Shapes
│ └── 'GSM7020543_A2_OB_virgin': GeoDataFrame shape: (2540, 2) (2D shapes)
└── Tables
└── 'table': AnnData (2540, 32285)
with coordinate systems:
▸ 'GSM7020543_A2_OB_virgin', with elements:
GSM7020543_A2_OB_virgin_hires_image (Images), GSM7020543_A2_OB_virgin (Shapes)
▸ 'GSM7020543_A2_OB_virgin_downscaled_hires', with elements:
GSM7020543_A2_OB_virgin_hires_image (Images), GSM7020543_A2_OB_virgin (Shapes)
▸ 'GSM7020543_A2_OB_virgin_downscaled_lowres', with elements:
GSM7020543_A2_OB_virgin (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("mgslqVWg6bpJ7lvq0000")
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("mgslqVWg6bpJ7lvq") # 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 mgslqVWg6bpJ7lvq0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/mgslqVWg6bpJ7lvq
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid mgslqVWg6bpJ7lvqLicense: NCBI GEO policy
Part of collection
PREGNANCY-RESPONSIVE POOLS OF ADULT NEURAL STEM CELLS FOR TRANSIENT NEUROGENESIS IN MOTHERS→ 4 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations (spots)
- 2,540
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,753 px
- mpp
- 4.093 µm/px
- Size
- 40.0 MB
- Sample ID
- GSM7020543
- License
- NCBI GEO policy
- Published
- Nov 22, 2023
Cite this dataset
doi.org/10.1126/science.abo5199 ↗ BibTeX
@article{Chaker_2023,
title = {Pregnancy-responsive pools of adult neural stem cells for transient neurogenesis in mothers},
volume = {382},
ISSN = {1095-9203},
url = {http://dx.doi.org/10.1126/science.abo5199},
DOI = {10.1126/science.abo5199},
number = {6673},
journal = {Science},
publisher = {American Association for the Advancement of Science (AAAS)},
author = {Chaker, Zayna and Segalada, Corina and Kretz, Jonas A. and Acar, Ilhan E. and Delgado, Ana C. and Crotet, Valerie and Moor, Andreas E. and Doetsch, Fiona},
year = {2023},
month = Nov,
pages = {958–963}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB