Visium
Mouse lung
GSM8995843
silver Interactive viewer H&E mycobacterial infectious disease ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ ├── 'GSM8995843_ATG7_WT_full_image': DataTree[cyx] (3, 3000, 3000), (3, 1500, 1500), (3, 750, 750), (3, 375, 375), (3, 187, 187)
│ ├── 'GSM8995843_ATG7_WT_hires_image': DataArray[cyx] (3, 2000, 1902)
│ └── 'GSM8995843_ATG7_WT_lowres_image': DataArray[cyx] (3, 600, 571)
├── Shapes
│ └── 'GSM8995843_ATG7_WT': GeoDataFrame shape: (3170, 2) (2D shapes)
└── Tables
└── 'table': AnnData (3170, 19465)
with coordinate systems:
▸ 'GSM8995843_ATG7_WT', with elements:
GSM8995843_ATG7_WT_full_image (Images), GSM8995843_ATG7_WT_hires_image (Images), GSM8995843_ATG7_WT_lowres_image (Images), GSM8995843_ATG7_WT (Shapes)
▸ 'GSM8995843_ATG7_WT_downscaled_hires', with elements:
GSM8995843_ATG7_WT_hires_image (Images), GSM8995843_ATG7_WT (Shapes)
▸ 'GSM8995843_ATG7_WT_downscaled_lowres', with elements:
GSM8995843_ATG7_WT_lowres_image (Images), GSM8995843_ATG7_WT (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("Vx3aP7i2MP8abzxU") # 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 Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/Vx3aP7i2MP8abzxU
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid Vx3aP7i2MP8abzxU Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["Vx3aP7i2MP8abzxU0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Spatial transcriptomics of Atg7 knockout mice reveals ATG7’s role in antimicrobial immunity against nontuberculous mycobacteria→ 2 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- lung
- Condition
- mycobacterial infectious disease
- Modality
- RNA
- Observations
- 3,170
- Tier
- silver
- Chemistry
- Visium CytAssist v2
- Resolution
- 1,902 × 2,000 px
- mpp
- 3.586 µm/px
- Size
- 78 MB
- Sample ID
- GSM8995843
- License
- NCBI GEO policy
- Published
- Jul 9, 2025
Cite this dataset
doi.org/10.1038/s41467-025-61791-1 ↗ BibTeX
@article{Jeon_2025,
title = {ATG7 in innate immune cells is required for host defense against nontuberculous mycobacterial pulmonary infections},
volume = {16},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-025-61791-1},
DOI = {10.1038/s41467-025-61791-1},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Jeon, Sang Min and Lee, Yeon Ju and Lee, Sang-Hee and Kim, Soo In and Lee, Bomi and Roh, Taylor and Kim, Young Jae and Kim, Hyeon Ji and Kim, In Soo and Whang, Jake and Kim, So-young and Jhun, Byung Woo and Chung, Chaeuk and Kang, Da Hyun and Yeo, Min-Kyung and Kim, Jin-Man and Jang, Jichan and Min, Jung-Joon and Komatsu, Masaaki and Kim, Jin Kyung and Park, Woong-Yang and Jo, Eun-Kyeong},
year = {2025},
month = July
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB