Visium

Mouse intestine

GSM7840108

bronze Interactive viewer H&E Provisional

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM7840108_V11Y11-298_A_hires_image': DataArray[cyx] (3, 1807, 2000)
│     └── 'GSM7840108_V11Y11-298_A_lowres_image': DataArray[cyx] (3, 542, 600)
├── Shapes
│     └── 'GSM7840108_V11Y11-298_A': GeoDataFrame shape: (3049, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (3049, 32285)
with coordinate systems:
    ▸ 'GSM7840108_V11Y11-298_A', with elements:
        GSM7840108_V11Y11-298_A_hires_image (Images), GSM7840108_V11Y11-298_A_lowres_image (Images), GSM7840108_V11Y11-298_A (Shapes)
    ▸ 'GSM7840108_V11Y11-298_A_downscaled_hires', with elements:
        GSM7840108_V11Y11-298_A_hires_image (Images), GSM7840108_V11Y11-298_A (Shapes)
    ▸ 'GSM7840108_V11Y11-298_A_downscaled_lowres', with elements:
        GSM7840108_V11Y11-298_A_lowres_image (Images), GSM7840108_V11Y11-298_A (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("R8OZ30zjplk6199b0000")
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("R8OZ30zjplk6199b")   # 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 R8OZ30zjplk6199b0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/R8OZ30zjplk6199b

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid R8OZ30zjplk6199b

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Spatially restricted immune and microbiota-driven adaptation of the gut [Spatial Transcriptomics]→

45 datasets · comparison

Metadata

Technology: Visium
Organism: mouse
Tissue: intestine
Modality: RNA
Observations (spots): 3,049
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 2,000 × 1,807 px
mpp: 4.638 µm/px
Size: 45.3 MB
Sample ID: GSM7840108
License: NCBI GEO policy
Published: Nov 26, 2024

Cite this dataset

doi.org/10.1038/s41586-024-08216-z ↗

BibTeX

@article{Mayassi_2024,
  title = {Spatially restricted immune and microbiota-driven adaptation of the gut},
  volume = {636},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/s41586-024-08216-z},
  DOI = {10.1038/s41586-024-08216-z},
  number = {8042},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Mayassi, Toufic and Li, Chenhao and Segerstolpe, Åsa and Brown, Eric M. and Weisberg, Rebecca and Nakata, Toru and Yano, Hiroshi and Herbst, Paula and Artis, David and Graham, Daniel B. and Xavier, Ramnik J.},
  year = {2024},
  month = Nov,
  pages = {447–456}
}

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