Visium

Human urinary bladder

NCBI854

silver Interactive viewer H&E bladder transitional cell carcinoma ✓ Verified publication

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI854_full_image': DataTree[cyx] (3, 13447, 14054), (3, 6723, 7027), (3, 3361, 3513), (3, 1680, 1756)
├── Shapes
│     └── 'NCBI854_spots': GeoDataFrame shape: (699, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (699, 17787)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI854_full_image (Images), NCBI854_spots (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Q1Tf6PPtg5uikwHU")   # 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/Q1Tf6PPtg5uikwHU

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Q1Tf6PPtg5uikwHU

Load with the Python client

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

ds = Catalog().cohort(uids=["Q1Tf6PPtg5uikwHU0000"])[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

Batf3-dendritic cells and 4-1BB-4-1BB ligand axis are required at the effector phase within the tumor microenvironment for PD-1-PD-L1 blockade efficacy→

2 datasets · replicates

Metadata

Technology: Visium
Organism: human
Tissue: urinary bladder
Condition: bladder transitional cell carcinoma
Modality: RNA
Observations: 699
Tier: silver
Chemistry: Visium v1
Resolution: 14,054 × 13,447 px
mpp: 0.623 µm/px
Size: 390 MB
Sample ID: NCBI854
License: CC BY-NC-SA 4.0 NonCommercial
Published: May 13, 2024

Cite this dataset

doi.org/10.1016/j.celrep.2024.114141 ↗

BibTeX

@article{Ziblat_2024,
  title = {Batf3+ DCs and the 4-1BB/4-1BBL axis are required at the effector phase in the tumor microenvironment for PD-1/PD-L1 blockade efficacy},
  volume = {43},
  ISSN = {2211-1247},
  url = {http://dx.doi.org/10.1016/j.celrep.2024.114141},
  DOI = {10.1016/j.celrep.2024.114141},
  number = {5},
  journal = {Cell Reports},
  publisher = {Elsevier BV},
  author = {Ziblat, Andrea and Horton, Brendan L. and Higgs, Emily F. and Hatogai, Ken and Martinez, Anna and Shapiro, Jason W. and Kim, Danny E.C. and Zha, YuanYuan and Sweis, Randy F. and Gajewski, Thomas F.},
  year = {2024},
  month = May,
  pages = {114141}
}

Source: sciencedirect.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB