Visium
Mouse eye
NCBI435
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI435_full_image': DataTree[cyx] (3, 10828, 10612), (3, 5414, 5306), (3, 2707, 2653), (3, 1353, 1326)
├── Shapes
│ └── 'NCBI435_spots': GeoDataFrame shape: (1106, 2) (2D shapes)
└── Tables
└── 'table': AnnData (1106, 32285)
with coordinate systems:
▸ 'global', with elements:
NCBI435_full_image (Images), NCBI435_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("TRp86aypNzNgq3jv") # 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/TRp86aypNzNgq3jv
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid TRp86aypNzNgq3jv Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["TRp86aypNzNgq3jv0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
Visium spatial transcriptomics analysis of lacrimal gland during chronic inflammation progression.→ 4 datasets · comparison
Metadata
- Technology
- Visium
- Organism
- mouse
- Tissue
- eye
- Modality
- RNA
- Observations
- 1,106
- Tier
- silver
- Chemistry
- Visium v1
- Resolution
- 10,612 × 10,828 px
- mpp
- 0.752 µm/px
- Size
- 217 MB
- Sample ID
- NCBI435
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Sep 23, 2022
Cite this dataset
doi.org/10.3389/fimmu.2022.1011125 ↗ BibTeX
@article{Mauduit_2022,
title = {Spatial transcriptomics of the lacrimal gland features macrophage activity and epithelium metabolism as key alterations during chronic inflammation},
volume = {13},
ISSN = {1664-3224},
url = {http://dx.doi.org/10.3389/fimmu.2022.1011125},
DOI = {10.3389/fimmu.2022.1011125},
journal = {Frontiers in Immunology},
publisher = {Frontiers Media SA},
author = {Mauduit, Olivier and Delcroix, Vanessa and Umazume, Takeshi and de Paiva, Cintia S. and Dartt, Darlene A. and Makarenkova, Helen P.},
year = {2022},
month = Oct
}Source: NCBI GEO ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB