Visium

Mouse tibia

GSM6733378

bronze Interactive viewer H&E Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM6733378_hires_image': DataArray[cyx] (3, 2000, 1966)
│     └── 'GSM6733378_lowres_image': DataArray[cyx] (3, 600, 590)
├── Shapes
│     └── 'GSM6733378': GeoDataFrame shape: (3335, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (3335, 19465)
with coordinate systems:
    ▸ 'GSM6733378', with elements:
        GSM6733378_hires_image (Images), GSM6733378_lowres_image (Images), GSM6733378 (Shapes)
    ▸ 'GSM6733378_downscaled_hires', with elements:
        GSM6733378_hires_image (Images), GSM6733378 (Shapes)
    ▸ 'GSM6733378_downscaled_lowres', with elements:
        GSM6733378_lowres_image (Images), GSM6733378 (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("zXDJQ3Ha8WueAnSR0000")
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("zXDJQ3Ha8WueAnSR")   # 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 zXDJQ3Ha8WueAnSR0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/zXDJQ3Ha8WueAnSR

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid zXDJQ3Ha8WueAnSR

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection

Spatial transcriptomic analysis of a pre-clinical NF1 pseudarthrosis fracture model→

2 datasets · other

Metadata

Technology: Visium
Organism: mouse
Tissue: tibia
Modality: RNA
Observations (spots): 3,335
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 1,966 × 2,000 px
mpp: 3.641 µm/px
Size: 34.3 MB
Sample ID: GSM6733378
License: NCBI GEO policy
Published: Jul 12, 2024

Cite this dataset

doi.org/10.1172/jci.insight.176802 ↗

BibTeX

@article{Rios_2024,
  title = {Spatial transcriptomics implicates impaired BMP signaling in NF1 fracture pseudarthrosis in murine and patient tissues},
  volume = {9},
  ISSN = {2379-3708},
  url = {http://dx.doi.org/10.1172/jci.insight.176802},
  DOI = {10.1172/jci.insight.176802},
  number = {16},
  journal = {JCI Insight},
  publisher = {American Society for Clinical Investigation},
  author = {Rios, Jonathan J. and Juan, Conan and Shelton, John M. and Paria, Nandina and Oxendine, Ila and Wassell, Meghan and Kidane, Yared H. and Cornelia, Reuel and Jeffery, Elise C. and Podeszwa, David A. and Conway, Simon J. and Wise, Carol A. and Tower, Robert J.},
  year = {2024},
  month = July
}

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