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Visium

Human gut-associated lymphoid tissue

GSM7986082

bronze Interactive viewer H&E Provisional
Human gut-associated lymphoid tissue preview
print(sdata) 
SpatialData object
├── Images
│     ├── 'GSM7986082_D1_hires_image': DataArray[cyx] (3, 1979, 2000)
│     └── 'GSM7986082_D1_lowres_image': DataArray[cyx] (3, 594, 600)
├── Shapes
│     └── 'GSM7986082_D1': GeoDataFrame shape: (2351, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (2351, 17943)
with coordinate systems:
    ▸ 'GSM7986082_D1', with elements:
        GSM7986082_D1_hires_image (Images), GSM7986082_D1_lowres_image (Images), GSM7986082_D1 (Shapes)
    ▸ 'GSM7986082_D1_downscaled_hires', with elements:
        GSM7986082_D1_hires_image (Images), GSM7986082_D1 (Shapes)
    ▸ 'GSM7986082_D1_downscaled_lowres', with elements:
        GSM7986082_D1_lowres_image (Images), GSM7986082_D1 (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("AJ4r2eQKBpR68Nry0000")
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("AJ4r2eQKBpR68Nry")   # 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 AJ4r2eQKBpR68Nry0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/AJ4r2eQKBpR68Nry

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid AJ4r2eQKBpR68Nry
Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue
Part of collection
Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue→
2 datasets · other

Metadata

Technology
Visium
Organism
human
Tissue
gut-associated lymphoid tissue
Modality
RNA
Observations (spots)
2,351
Tier
bronze
Chemistry
Visium v1
Magnification
other
Resolution
2,000 × 1,979 px
mpp
3.345 µm/px
Size
10.5 MB
Sample ID
GSM7986082
License
NCBI GEO policy
Published
Mar 28, 2024

Cite this dataset

doi.org/10.1038/s41467-024-48267-4 ↗
BibTeX 
@article{Montorsi_2024,
  title = {Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue},
  volume = {15},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-024-48267-4},
  DOI = {10.1038/s41467-024-48267-4},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Montorsi, Lucia and Pitcher, Michael J. and Zhao, Yuan and Dionisi, Chiara and Demonti, Alicia and Tull, Thomas J. and Dhami, Pawan and Ellis, Richard J. and Bishop, Cynthia and Sanderson, Jeremy D. and Jain, Sahil and D’Cruz, David and Gibbons, Deena L. and Winkler, Thomas H. and Bemark, Mats and Ciccarelli, Francesca D. and Spencer, Jo},
  year = {2024},
  month = May
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB