Visium
Mouse esophagus
GSM8385443
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8385443_E16_5_hires_image': DataArray[cyx] (3, 1856, 2000)
│ └── 'GSM8385443_E16_5_lowres_image': DataArray[cyx] (3, 557, 600)
├── Shapes
│ └── 'GSM8385443_E16_5': GeoDataFrame shape: (3593, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3593, 32285)
with coordinate systems:
▸ 'GSM8385443_E16_5', with elements:
GSM8385443_E16_5_hires_image (Images), GSM8385443_E16_5_lowres_image (Images), GSM8385443_E16_5 (Shapes)
▸ 'GSM8385443_E16_5_downscaled_hires', with elements:
GSM8385443_E16_5_hires_image (Images), GSM8385443_E16_5 (Shapes)
▸ 'GSM8385443_E16_5_downscaled_lowres', with elements:
GSM8385443_E16_5_lowres_image (Images), GSM8385443_E16_5 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("NFNycJJFEGKKO0sQ0000")
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("NFNycJJFEGKKO0sQ") # 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 NFNycJJFEGKKO0sQ0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/NFNycJJFEGKKO0sQ
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid NFNycJJFEGKKO0sQLicense: NCBI GEO policy
Part of collection
Lgr5 Marks Stem/Progenitor Cells Contributing to Epithelial and Muscle Development in the Mouse Esophagus→ 4 datasets · time course
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- esophagus
- Modality
- RNA
- Observations (spots)
- 3,593
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,856 px
- mpp
- 3.920 µm/px
- Size
- 83.1 MB
- Sample ID
- GSM8385443
- License
- NCBI GEO policy
- Published
- Jul 22, 2024
Cite this dataset
doi.org/10.1038/s41467-024-51559-4 ↗ BibTeX
@article{Kostic_2024,
title = {Lgr5 marks stem/progenitor cells contributing to epithelial and muscle development in the mouse esophagus},
volume = {15},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-024-51559-4},
DOI = {10.1038/s41467-024-51559-4},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Kostic, Lana and Leung, Carly and Ahmad Murad, Katzrin and Kancheva, Snezhina and Perna, Stefano and Lee, Bernett and Barker, Nick},
year = {2024},
month = Aug
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB