spatial transcriptomics

Human prostate gland

MEND18

bronze Interactive viewer H&E prostate cancer ✓ Verified publication

Preview Client Lamin CLI

print(sdata)

SpatialData object
├── Images
│     └── 'MEND18_full_image': DataTree[cyx] (3, 29184, 32768), (3, 14592, 16384), (3, 7296, 8192), (3, 3648, 4096)
├── Shapes
│     └── 'MEND18_spots': GeoDataFrame shape: (209, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (209, 16016)
with coordinate systems:
    ▸ 'global', with elements:
        MEND18_full_image (Images), MEND18_spots (Shapes)

Install (Python 3.12+) Docs →

Python · sddb client

from sddb import Catalog

ds = Catalog().dataset("J44OEqwwnP0U8PnJ0000")
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("J44OEqwwnP0U8PnJ")   # 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 J44OEqwwnP0U8PnJ0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/J44OEqwwnP0U8PnJ

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid J44OEqwwnP0U8PnJ

Install (Python 3.12+) Docs →

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

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Part of collection

Prostate needle biopsies pre- and post-ADT: Count matrices, histological-, and Androgen receptor immunohistochemistry images→

24 datasets · comparison

Metadata

Technology: spatial transcriptomics
Organism: human
Tissue: prostate gland
Condition: prostate cancer
Modality: RNA
Observations (spots): 209
Tier: bronze
Chemistry: ST 1k
Magnification: 40x
Resolution: 32,768 × 29,184 px
mpp: 0.275 µm/px
Size: 955 MB
Sample ID: MEND18
License: CC BY-NC-SA 4.0 NonCommercial
Published: Jul 20, 2022

Cite this dataset

doi.org/10.1038/s41467-022-33069-3 ↗

BibTeX

@article{Marklund_2022,
  title = {Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones},
  volume = {13},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-022-33069-3},
  DOI = {10.1038/s41467-022-33069-3},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Marklund, Maja and Schultz, Niklas and Friedrich, Stefanie and Berglund, Emelie and Tarish, Firas and Tanoglidi, Anna and Liu, Yao and Bergenstråhle, Ludvig and Erickson, Andrew and Helleday, Thomas and Lamb, Alastair D. and Sonnhammer, Erik and Lundeberg, Joakim},
  year = {2022},
  month = Sept
}

Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB