Visium HD

Mouse kidney

GSM8662446

silver Interactive viewer H&E ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     ├── 'GSM8662446_square_008um_cytassist_image': DataArray[cyx] (3, 3000, 3200)
│     ├── 'GSM8662446_square_008um_hires_image': DataArray[cyx] (3, 5609, 6000)
│     └── 'GSM8662446_square_008um_lowres_image': DataArray[cyx] (3, 561, 600)
├── Shapes
│     ├── 'GSM8662446_square_008um_square_002um': GeoDataFrame shape: (4717408, 1) (2D shapes)
│     ├── 'GSM8662446_square_008um_square_008um': GeoDataFrame shape: (302036, 1) (2D shapes)
│     ├── 'GSM8662446_square_008um_square_016um': GeoDataFrame shape: (77975, 1) (2D shapes)
│     └── 'GSM8662446_square_008um_square_016um_for_vitessce': GeoDataFrame shape: (77975, 2) (2D shapes)
└── Tables
      ├── 'square_002um': AnnData (4717408, 19059)
      ├── 'square_008um': AnnData (302036, 19059)
      └── 'square_016um': AnnData (77975, 19059)
with coordinate systems:
    ▸ 'GSM8662446_square_008um', with elements:
        GSM8662446_square_008um_cytassist_image (Images), GSM8662446_square_008um_hires_image (Images), GSM8662446_square_008um_lowres_image (Images), GSM8662446_square_008um_square_002um (Shapes), GSM8662446_square_008um_square_008um (Shapes), GSM8662446_square_008um_square_016um (Shapes), GSM8662446_square_008um_square_016um_for_vitessce (Shapes)
    ▸ 'GSM8662446_square_008um_downscaled_hires', with elements:
        GSM8662446_square_008um_hires_image (Images), GSM8662446_square_008um_square_002um (Shapes), GSM8662446_square_008um_square_008um (Shapes), GSM8662446_square_008um_square_016um (Shapes), GSM8662446_square_008um_square_016um_for_vitessce (Shapes)
    ▸ 'GSM8662446_square_008um_downscaled_lowres', with elements:
        GSM8662446_square_008um_lowres_image (Images), GSM8662446_square_008um_square_002um (Shapes), GSM8662446_square_008um_square_008um (Shapes), GSM8662446_square_008um_square_016um (Shapes), GSM8662446_square_008um_square_016um_for_vitessce (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("HVKVnPeTrMFTx9Ty0000")
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("HVKVnPeTrMFTx9Ty")   # 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 HVKVnPeTrMFTx9Ty0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/HVKVnPeTrMFTx9Ty

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid HVKVnPeTrMFTx9Ty

Install (Python 3.12+) Docs →

License: NCBI GEO policy

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

Part of collection

Gain-of-function ENL YEATS domain mutations impede nephrogenesis through gene expression control [Spatial Transcriptomics]→

2 datasets · comparison

Metadata

Technology: Visium HD
Organism: mouse
Tissue: kidney
Modality: RNA
Observations (bins): 302,036
Tier: silver
Resolution: 6,000 × 5,609 px
mpp: 1.338 µm/px
Size: 2.1 GB
Sample ID: GSM8662446
License: NCBI GEO policy
Published: Feb 20, 2025

Cite this dataset

doi.org/10.1038/s41467-025-57926-z ↗

BibTeX

@article{Xue_2025,
  title = {Expression of ENL YEATS domain tumor mutations in nephrogenic or stromal lineage impairs kidney development},
  volume = {16},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-025-57926-z},
  DOI = {10.1038/s41467-025-57926-z},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Xue, Zhaoyu and Xuan, Hongwen and Lau, Kin and Su, Yangzhou and Wegener, Marc and Li, Kuai and Turner, Lisa and Adams, Marie and Shi, Xiaobing and Wen, Hong},
  year = {2025},
  month = Mar
}

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