Visium
Human lymphoid tissue
GSM8442679
bronze Interactive viewer H&E non-Hodgkin lymphoma Provisional
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8442679_Luf4_hires_image': DataArray[cyx] (3, 1841, 2000)
│ └── 'GSM8442679_Luf4_lowres_image': DataArray[cyx] (3, 553, 600)
├── Shapes
│ └── 'GSM8442679_Luf4': GeoDataFrame shape: (13945, 2) (2D shapes)
└── Tables
└── 'table': AnnData (13945, 18085)
with coordinate systems:
▸ 'GSM8442679_Luf4', with elements:
GSM8442679_Luf4_hires_image (Images), GSM8442679_Luf4_lowres_image (Images), GSM8442679_Luf4 (Shapes)
▸ 'GSM8442679_Luf4_downscaled_hires', with elements:
GSM8442679_Luf4_hires_image (Images), GSM8442679_Luf4 (Shapes)
▸ 'GSM8442679_Luf4_downscaled_lowres', with elements:
GSM8442679_Luf4_lowres_image (Images), GSM8442679_Luf4 (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("7yKJs51NK6sL5Ikw0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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("7yKJs51NK6sL5Ikw") # 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 Shell
# sddb client: download the .zarr into data/
sddb-cli download 7yKJs51NK6sL5Ikw0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/7yKJs51NK6sL5Ikw
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 7yKJs51NK6sL5IkwLicense: NCBI GEO policy
Part of collection
Spatial transcriptomics of HIV-associated non-Hodgkin lymphomas by EBV status and cell of origin→ 10 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- human
- Tissue
- lymphoid tissue
- Condition
- non-Hodgkin lymphoma
- Modality
- RNA
- Observations (spots)
- 13,945
- Tier
- bronze
- Chemistry
- Visium v1
- Resolution
- 2,000 × 1,841 px
- mpp
- 7.732 µm/px
- Size
- 214 MB
- Sample ID
- GSM8442679
- License
- NCBI GEO policy
- Published
- Feb 18, 2026
Cite this dataset
doi.org/10.1101/2025.10.15.682084 ↗ BibTeX
@article{Chadburn_2025,
title = {HIV-associated non-Hodgkin lymphoma tumor-microenvironment axes differ by EBV status across cellular origins},
url = {http://dx.doi.org/10.1101/2025.10.15.682084},
DOI = {10.1101/2025.10.15.682084},
publisher = {openRxiv},
author = {Chadburn, Amy and Aguilar Hernandez, Maria Montserrat and Dai, Joanne and Harrison, Mitra and Reinoso-Vizcaino, Nicolas M. and Barry, Ashley P. and Hocke, Emily and Abramson, Karen and Jain, Vaibhav and Chan, Cliburn and Cesarman, Ethel and Luftig, Micah A. and SoRelle, Elliott D.},
year = {2025},
month = Oct
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB