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Visium

Mouse caudate nucleus

GSM7392325

bronze Interactive viewer H&E Parkinson disease Provisional
Mouse caudate nucleus preview
print(sdata) 
SpatialData object
├── Images
│     └── 'GSM7392325_V11T17-102_A1_RNA_hires_image': DataArray[cyx] (3, 1937, 2000)
├── Shapes
│     └── 'GSM7392325_V11T17-102_A1_RNA': GeoDataFrame shape: (4968, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (4968, 17943)
with coordinate systems:
    ▸ 'GSM7392325_V11T17-102_A1_RNA', with elements:
        GSM7392325_V11T17-102_A1_RNA_hires_image (Images), GSM7392325_V11T17-102_A1_RNA (Shapes)
    ▸ 'GSM7392325_V11T17-102_A1_RNA_downscaled_hires', with elements:
        GSM7392325_V11T17-102_A1_RNA_hires_image (Images), GSM7392325_V11T17-102_A1_RNA (Shapes)
    ▸ 'GSM7392325_V11T17-102_A1_RNA_downscaled_lowres', with elements:
        GSM7392325_V11T17-102_A1_RNA (Shapes)
Load in Python 
import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("TO4AXFtoWfxqcXi3")   # 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/TO4AXFtoWfxqcXi3

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid TO4AXFtoWfxqcXi3
Load with the Python client 
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog

ds = Catalog().cohort(uids=["TO4AXFtoWfxqcXi30000"])[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
caudate nucleus
Condition
Parkinson disease
Modality
RNA
Observations
4,968
Tier
bronze
Chemistry
Visium v1
Magnification
other
Resolution
2,000 × 1,937 px
mpp
3.537 µm/px
Size
16 MB
Sample ID
GSM7392325
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