Visium

Mouse sagittal suture

GSM5291685

bronze Interactive viewer H&E Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM5291685_C1_hires_image': DataArray[cyx] (3, 2000, 2000)
│     └── 'GSM5291685_C1_lowres_image': DataArray[cyx] (3, 600, 600)
├── Shapes
│     └── 'GSM5291685_C1': GeoDataFrame shape: (560, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (560, 31053)
with coordinate systems:
    ▸ 'GSM5291685_C1', with elements:
        GSM5291685_C1_hires_image (Images), GSM5291685_C1_lowres_image (Images), GSM5291685_C1 (Shapes)
    ▸ 'GSM5291685_C1_downscaled_hires', with elements:
        GSM5291685_C1_hires_image (Images), GSM5291685_C1 (Shapes)
    ▸ 'GSM5291685_C1_downscaled_lowres', with elements:
        GSM5291685_C1_lowres_image (Images), GSM5291685_C1 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("MCQDcnxGwTStIHXq0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)

Install (Python 3.12+) Docs →

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("MCQDcnxGwTStIHXq")   # 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

Install (Python 3.12+) Docs →

Shell

# sddb client: download the .zarr into data/
sddb-cli download MCQDcnxGwTStIHXq0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/MCQDcnxGwTStIHXq

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid MCQDcnxGwTStIHXq

Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue

Part of collection

Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGFβ signaling→

4 datasets · other

Metadata

Technology: Visium
Organism: mouse
Tissue: sagittal suture
Modality: RNA
Observations (spots): 560
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 2,000 px
mpp: 3.412 µm/px
Size: 14.8 MB
Sample ID: GSM5291685
License: NCBI GEO policy
Published: Sep 29, 2021

Cite this dataset

doi.org/10.1073/pnas.2103087118 ↗

BibTeX

@article{Tower_2021,
  title = {Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling},
  volume = {118},
  ISSN = {1091-6490},
  url = {http://dx.doi.org/10.1073/pnas.2103087118},
  DOI = {10.1073/pnas.2103087118},
  number = {42},
  journal = {Proceedings of the National Academy of Sciences},
  publisher = {National Academy of Sciences},
  author = {Tower, Robert J. and Li, Zhu and Cheng, Yu-Hao and Wang, Xue-Wei and Rajbhandari, Labchan and Zhang, Qian and Negri, Stefano and Uytingco, Cedric R. and Venkatesan, Arun and Zhou, Feng-Quan and Cahan, Patrick and James, Aaron W. and Clemens, Thomas L.},
  year = {2021},
  month = Oct
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB