Visium
Mouse diaphragm
GSM7804885
bronze Interactive viewer H&E Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM7804885_control_E14_2_hires_image': DataArray[cyx] (3, 2000, 1998)
│ └── 'GSM7804885_control_E14_2_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│ └── 'GSM7804885_control_E14_2': GeoDataFrame shape: (842, 2) (2D shapes)
└── Tables
└── 'table': AnnData (842, 19465)
with coordinate systems:
▸ 'GSM7804885_control_E14_2', with elements:
GSM7804885_control_E14_2_hires_image (Images), GSM7804885_control_E14_2_lowres_image (Images), GSM7804885_control_E14_2 (Shapes)
▸ 'GSM7804885_control_E14_2_downscaled_hires', with elements:
GSM7804885_control_E14_2_hires_image (Images), GSM7804885_control_E14_2 (Shapes)
▸ 'GSM7804885_control_E14_2_downscaled_lowres', with elements:
GSM7804885_control_E14_2_lowres_image (Images), GSM7804885_control_E14_2 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("SxyUHPBPPz3tt5XA0000")
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("SxyUHPBPPz3tt5XA") # 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 SxyUHPBPPz3tt5XA0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/SxyUHPBPPz3tt5XA
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid SxyUHPBPPz3tt5XALicense: NCBI GEO policy
Part of collection
Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression→ 8 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- diaphragm
- Modality
- RNA
- Observations (spots)
- 842
- Tier
- bronze
- Chemistry
- Visium v1
- Magnification
- other
- Resolution
- 1,998 × 2,000 px
- mpp
- 3.713 µm/px
- Size
- 24.5 MB
- Sample ID
- GSM7804885
- License
- NCBI GEO policy
- Published
- May 23, 2024
Cite this dataset
doi.org/10.1016/j.isci.2024.110018 ↗ BibTeX
@article{Kaplan_2024,
title = {Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression},
volume = {27},
ISSN = {2589-0042},
url = {http://dx.doi.org/10.1016/j.isci.2024.110018},
DOI = {10.1016/j.isci.2024.110018},
number = {6},
journal = {iScience},
publisher = {Elsevier BV},
author = {Kaplan, Mehmet Mahsum and Zeidler, Maximilian and Knapp, Annabella and Hölzl, Martina and Kress, Michaela and Fritsch, Helga and Krogsdam, Anne and Flucher, Bernhard E.},
year = {2024},
month = June,
pages = {110018}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB