Visium

Human liver

NCBI643

silver Interactive viewer H&E hepatocellular carcinoma Provisional

Preview Download via Python Download via CLI Load via sddb

print(sdata)

SpatialData object
├── Images
│     └── 'NCBI643_full_image': DataTree[cyx] (3, 24936, 23848), (3, 12468, 11924), (3, 6234, 5962), (3, 3117, 2981)
├── Shapes
│     └── 'NCBI643_spots': GeoDataFrame shape: (2261, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2261, 36601)
with coordinate systems:
    ▸ 'global', with elements:
        NCBI643_full_image (Images), NCBI643_spots (Shapes)

Load in Python

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("FLnv2snJFpVti2P9")   # 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/FLnv2snJFpVti2P9

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid FLnv2snJFpVti2P9

Load with the Python client

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

ds = Catalog().cohort(uids=["FLnv2snJFpVti2P90000"])[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

Identification of TREM1+CD163+ myeloid cells as a deleterious immune subset in HCC [Spatial Transcriptomics]→

2 datasets · replicates

Metadata

Technology: Visium
Organism: human
Tissue: liver
Condition: hepatocellular carcinoma
Modality: RNA
Observations: 2,261
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 23,848 × 24,936 px
mpp: 0.454 µm/px
Size: 716 MB
Sample ID: NCBI643
License: CC BY-NC-SA 4.0 NonCommercial
Published: Feb 4, 2024

Cite this dataset

doi.org/10.1101/2022.11.09.515839 ↗

BibTeX

@article{Giraud_2022,
  title = {TREM1
                  <sup>+</sup>
                  regulatory myeloid cells expand in steatohepatitis-HCC and associate with poor prognosis and therapeutic resistance to immune checkpoint blockade},
  url = {http://dx.doi.org/10.1101/2022.11.09.515839},
  DOI = {10.1101/2022.11.09.515839},
  publisher = {openRxiv},
  author = {Giraud, Julie and Chalopin, Domitille and Ramel, Eloïse and Boyer, Thomas and Zouine, Atika and Derieppe, Marie-Alix and Larmonier, Nicolas and Adotevi, Olivier and Bail, Brigitte Le and Blanc, Jean-Frédéric and Chiche, Laurence and Nikolski, Macha and Saleh, Maya},
  year = {2022},
  month = Nov
}

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