Visium

Human liver

NCBI643

silver Interactive viewer H&E hepatocellular carcinoma Provisional

Preview Client Lamin CLI

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)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("FLnv2snJFpVti2P90000")
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("FLnv2snJFpVti2P9")   # 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 FLnv2snJFpVti2P90000 --dest data/

# or lamin: 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

Install (Python 3.12+) Docs →

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

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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 (spots): 2,261
Tier: silver
Chemistry: Visium v1
Magnification: 20x
Resolution: 23,848 × 24,936 px
mpp: 0.454 µm/px
Size: 750 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