Visium
Mouse trunk
GSM4861203
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'GSM4861203_Visium-B1_hires_image': DataArray[cyx] (3, 2000, 1997)
├── Shapes
│ └── 'GSM4861203_Visium-B1': GeoDataFrame shape: (222, 2) (2D shapes)
└── Tables
└── 'table': AnnData (222, 53574)
with coordinate systems:
▸ 'GSM4861203_Visium-B1', with elements:
GSM4861203_Visium-B1_hires_image (Images), GSM4861203_Visium-B1 (Shapes)
▸ 'GSM4861203_Visium-B1_downscaled_hires', with elements:
GSM4861203_Visium-B1_hires_image (Images), GSM4861203_Visium-B1 (Shapes)
▸ 'GSM4861203_Visium-B1_downscaled_lowres', with elements:
GSM4861203_Visium-B1 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("lyqwdGBZ3d0OlAIv0000")
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("lyqwdGBZ3d0OlAIv") # 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 lyqwdGBZ3d0OlAIv0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/lyqwdGBZ3d0OlAIv
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid lyqwdGBZ3d0OlAIvLicense: NCBI GEO policy
Part of collection
Single cell- Cluster-RNA seq and Spatial Transcriptomics from the trunk of mouse embryos of different genotypes (wild type, Pax2-GFP, Pax2-GFP; Gata3 knockout) and developmental stages (E8.75, E9.5, E11.5) [Spatial Transcriptomics]→ 4 datasets · other
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- trunk
- Modality
- RNA
- Observations (spots)
- 222
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,997 × 2,000 px
- mpp
- 3.574 µm/px
- Size
- 4.4 MB
- Sample ID
- GSM4861203
- License
- NCBI GEO policy
- Published
- Feb 16, 2021
Cite this dataset
doi.org/10.1038/s41467-021-22931-5 ↗ BibTeX
@article{Sanchez_Ferras_2021,
title = {A coordinated progression of progenitor cell states initiates urinary tract development},
volume = {12},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-021-22931-5},
DOI = {10.1038/s41467-021-22931-5},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Sanchez-Ferras, Oraly and Pacis, Alain and Sotiropoulou, Maria and Zhang, Yuhong and Wang, Yu Chang and Bourgey, Mathieu and Bourque, Guillaume and Ragoussis, Jiannis and Bouchard, Maxime},
year = {2021},
month = May
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB