Visium

Human urinary bladder

NCBI854

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

Preview Client Lamin CLI

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)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("Q1Tf6PPtg5uikwHU0000")
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("Q1Tf6PPtg5uikwHU")   # 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 Q1Tf6PPtg5uikwHU0000 --dest data/

# or lamin: 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

Install (Python 3.12+) Docs →

License: CC BY-NC-SA 4.0 (noncommercial)

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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 (spots): 699
Tier: silver
Chemistry: Visium v1
Resolution: 14,054 × 13,447 px
mpp: 0.623 µm/px
Size: 409 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