Visium
Mouse growth plate cartilage
GSM8473629
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8473629_hires_image': DataArray[cyx] (3, 1819, 2000)
│ └── 'GSM8473629_lowres_image': DataArray[cyx] (3, 546, 600)
├── Shapes
│ └── 'GSM8473629': GeoDataFrame shape: (1852, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1852, 19465)
with coordinate systems:
▸ 'GSM8473629', with elements:
GSM8473629_hires_image (Images), GSM8473629_lowres_image (Images), GSM8473629 (Shapes)
▸ 'GSM8473629_downscaled_hires', with elements:
GSM8473629_hires_image (Images), GSM8473629 (Shapes)
▸ 'GSM8473629_downscaled_lowres', with elements:
GSM8473629_lowres_image (Images), GSM8473629 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("FzT9jQpEHugc6Dbh0000")
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("FzT9jQpEHugc6Dbh") # 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 FzT9jQpEHugc6Dbh0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/FzT9jQpEHugc6Dbh
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid FzT9jQpEHugc6DbhLicense: NCBI GEO policy
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- growth plate cartilage
- Modality
- RNA
- Observations (spots)
- 1,852
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 2,000 × 1,819 px
- mpp
- 4.046 µm/px
- Size
- 36.6 MB
- Sample ID
- GSM8473629
- License
- NCBI GEO policy
- Published
- Sep 19, 2024
Cite this dataset
doi.org/10.1093/jbmr/zjae144 ↗ BibTeX
@article{Bian_2024,
title = {The G protein-coupled receptor ADGRG6 maintains mouse growth plate homeostasis through IHH signaling},
volume = {39},
ISSN = {1523-4681},
url = {http://dx.doi.org/10.1093/jbmr/zjae144},
DOI = {10.1093/jbmr/zjae144},
number = {11},
journal = {Journal of Bone and Mineral Research},
publisher = {Oxford University Press (OUP)},
author = {Bian, Fangzhou and Hansen, Victoria and Feng, Hong Colleen and He, Jingyu and Chen, Yanshi and Feng, Kaining and Ebrahimi, Brenda and Gray, Ryan S and Chai, Yang and Wu, Chia-Lung and Liu, Zhaoyang},
year = {2024},
month = Sept,
pages = {1644–1658}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB