Visium

Mouse brain

GSM7392318

bronze Interactive viewer H&E Provisional

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     └── 'GSM7392318_V11T16-085_A1_RNA_hires_image': DataArray[cyx] (3, 2000, 1979)
├── Shapes
│     └── 'GSM7392318_V11T16-085_A1_RNA': GeoDataFrame shape: (2964, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2964, 32285)
with coordinate systems:
    ▸ 'GSM7392318_V11T16-085_A1_RNA', with elements:
        GSM7392318_V11T16-085_A1_RNA_hires_image (Images), GSM7392318_V11T16-085_A1_RNA (Shapes)
    ▸ 'GSM7392318_V11T16-085_A1_RNA_downscaled_hires', with elements:
        GSM7392318_V11T16-085_A1_RNA_hires_image (Images), GSM7392318_V11T16-085_A1_RNA (Shapes)
    ▸ 'GSM7392318_V11T16-085_A1_RNA_downscaled_lowres', with elements:
        GSM7392318_V11T16-085_A1_RNA (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("cAFMPWlyujEwi8uF")   # 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

Load from the CLI

# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/cAFMPWlyujEwi8uF

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid cAFMPWlyujEwi8uF

Load with the Python client

# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["cAFMPWlyujEwi8uF0000"])[0]
ds.elements()                 # inspect without downloading
sdata = ds.load(lazy=False)   # copy to the local cache and open

Docs: finding & loading data →

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

Part of collection

Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section→

18 datasets · time course

Metadata

Technology: Visium
Organism: mouse
Tissue: brain
Modality: RNA
Observations: 2,964
Tier: bronze
Chemistry: Visium v1
Magnification: other
Resolution: 1,979 × 2,000 px
mpp: 3.507 µm/px
Size: 26 MB
Sample ID: GSM7392318
License: unknown
Published: May 21, 2023

Cite this dataset

doi.org/10.1038/s41587-023-01937-y ↗

BibTeX

@article{Vicari_2023,
  title = {Spatial multimodal analysis of transcriptomes and metabolomes in tissues},
  volume = {42},
  ISSN = {1546-1696},
  url = {http://dx.doi.org/10.1038/s41587-023-01937-y},
  DOI = {10.1038/s41587-023-01937-y},
  number = {7},
  journal = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  author = {Vicari, Marco and Mirzazadeh, Reza and Nilsson, Anna and Shariatgorji, Reza and Bjärterot, Patrik and Larsson, Ludvig and Lee, Hower and Nilsson, Mats and Foyer, Julia and Ekvall, Markus and Czarnewski, Paulo and Zhang, Xiaoqun and Svenningsson, Per and Käll, Lukas and Andrén, Per E. and Lundeberg, Joakim},
  year = {2023},
  month = Sept,
  pages = {1046–1050}
}

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