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Visium

Human kidney

Mapping single cell transcriptomes in kidney cancer (6800STDY12499503)

bronze Interactive viewer H&E renal cell carcinoma Provisional
Visium
print(sdata) 
SpatialData object
├── Images
│     ├── 'spaceranger130_count_44316_6800STDY12499503_GRCh38-2020-A_hires': DataArray[cyx] (3, 1834, 2000)
│     └── 'spaceranger130_count_44316_6800STDY12499503_GRCh38-2020-A_lowres': DataArray[cyx] (3, 550, 600)
├── Shapes
│     └── 'locations': GeoDataFrame shape: (2661, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2661, 36601)
with coordinate systems:
    ▸ 'global', with elements:
        spaceranger130_count_44316_6800STDY12499503_GRCh38-2020-A_hires (Images), spaceranger130_count_44316_6800STDY12499503_GRCh38-2020-A_lowres (Images), locations (Shapes)
    ▸ 'spaceranger130_count_44316_6800STDY12499503_GRCh38-2020-A_hires', with elements:
        spaceranger130_count_44316_6800STDY12499503_GRCh38-2020-A_hires (Images), locations (Shapes)
    ▸ 'spaceranger130_count_44316_6800STDY12499503_GRCh38-2020-A_lowres', with elements:
        spaceranger130_count_44316_6800STDY12499503_GRCh38-2020-A_lowres (Images), locations (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("lDbPIhrK1OXIC4TJ0000")
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("lDbPIhrK1OXIC4TJ")   # 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 lDbPIhrK1OXIC4TJ0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/lDbPIhrK1OXIC4TJ

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid lDbPIhrK1OXIC4TJ
Install (Python 3.12+) Docs →

License: CC BY 4.0

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mendeley-g67bkbnhhg→
16 datasets · publication

Metadata

Technology
Visium
Vendor
10x Genomics
Organism
human
Tissue
kidney
Condition
renal cell carcinoma
Modality
RNA
Observations (spots)
2,661
Tier
bronze
Chemistry
Visium v1
Resolution
2,000 × 1,834 px
mpp
5.376 µm/px
Size
37.3 MB
Sample ID
g67bkbnhhg:6800STDY12499503
License
CC BY 4.0
Published
Oct 10, 2022

Cite this dataset

doi.org/10.17632/g67bkbnhhg.1 ↗
BibTeX 
@article{mendeley:g67bkbnhhg,
  doi = {10.17632/g67bkbnhhg.1},
  title = {Mapping single cell transcriptomes in kidney cancer (6800STDY12499413)},
  year = {2022}
}

Source: data.mendeley.com ↗ · License: CC BY 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB