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Visium

Human small intestine

GSM9078981

bronze Interactive viewer H&E small intestine neuroendocrine neoplasm Provisional
Human small intestine preview
print(sdata) 
SpatialData object
├── Images
│     ├── 'GSM9078981_V13B16-356_A1_hires_image': DataArray[cyx] (3, 1972, 2000)
│     └── 'GSM9078981_V13B16-356_A1_lowres_image': DataArray[cyx] (3, 592, 600)
├── Shapes
│     └── 'GSM9078981_V13B16-356_A1': GeoDataFrame shape: (1110, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (1110, 17943)
with coordinate systems:
    ▸ 'GSM9078981_V13B16-356_A1', with elements:
        GSM9078981_V13B16-356_A1_hires_image (Images), GSM9078981_V13B16-356_A1_lowres_image (Images), GSM9078981_V13B16-356_A1 (Shapes)
    ▸ 'GSM9078981_V13B16-356_A1_downscaled_hires', with elements:
        GSM9078981_V13B16-356_A1_hires_image (Images), GSM9078981_V13B16-356_A1 (Shapes)
    ▸ 'GSM9078981_V13B16-356_A1_downscaled_lowres', with elements:
        GSM9078981_V13B16-356_A1_lowres_image (Images), GSM9078981_V13B16-356_A1 (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("1OAGn4ASKu2rgROR0000")
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("1OAGn4ASKu2rgROR")   # 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 1OAGn4ASKu2rgROR0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/1OAGn4ASKu2rgROR

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 1OAGn4ASKu2rgROR
Install (Python 3.12+) Docs →

License: NCBI GEO policy

View on Lamin ↗ Open in Vitessce ↗ Flag a data issue
Part of collection
Spatial Transcriptomics Reveals Local Subtype-Specific Identity and Signaling within Multifocal Small Intestinal Neuroendocrine Tumors→
8 datasets · replicates

Metadata

Technology
Visium
Organism
human
Tissue
small intestine
Condition
small intestine neuroendocrine neoplasm
Modality
RNA
Observations (spots)
1,110
Tier
bronze
Chemistry
Visium v1
Resolution
2,000 × 1,972 px
mpp
3.576 µm/px
Size
11.8 MB
Sample ID
GSM9078981
License
NCBI GEO policy
Published
Feb 9, 2026

Cite this dataset

doi.org/10.1158/1078-0432.ccr-25-2854 ↗
BibTeX 
@article{Yogo_2026,
  title = {Spatial Transcriptomics Reveals Location-Specific Tumor Cell Subtypes and Signaling within Multifocal Small Intestinal Neuroendocrine Tumors},
  volume = {32},
  ISSN = {1557-3265},
  url = {http://dx.doi.org/10.1158/1078-0432.ccr-25-2854},
  DOI = {10.1158/1078-0432.ccr-25-2854},
  number = {10},
  journal = {Clinical Cancer Research},
  publisher = {American Association for Cancer Research (AACR)},
  author = {Yogo, Akitada and Akanuma, Naoki and Kim, Grace E. and Mäkinen, Netta and Thirlwell, Chrissie and Nakakura, Eric K.},
  year = {2026},
  month = Mar,
  pages = {2098–2109}
}

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