spatial transcriptomics
Mouse brain
NCBI344
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'NCBI344_full_image': DataTree[cyx] (3, 9878, 9324), (3, 4939, 4662), (3, 2469, 2331), (3, 1234, 1165)
├── Shapes
│ └── 'NCBI344_spots': GeoDataFrame shape: (406, 2) (2D shapes)
└── Tables
└── 'table': AnnData (406, 21473)
with coordinate systems:
▸ 'global', with elements:
NCBI344_full_image (Images), NCBI344_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("zpn8OoSiW3iYHJIf") # 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/zpn8OoSiW3iYHJIf
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid zpn8OoSiW3iYHJIf Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["zpn8OoSiW3iYHJIf0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openMetadata
- Technology
- spatial transcriptomics
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA
- Observations
- 406
- Tier
- silver
- Chemistry
- ST 1k
- Resolution
- 9,324 × 9,878 px
- mpp
- 0.691 µm/px
- Size
- 174 MB
- Sample ID
- NCBI344
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- May 3, 2020
Cite this dataset
doi.org/10.1126/sciadv.abb3446 ↗ BibTeX
@article{Ortiz_2020,
title = {Molecular atlas of the adult mouse brain},
volume = {6},
ISSN = {2375-2548},
url = {http://dx.doi.org/10.1126/sciadv.abb3446},
DOI = {10.1126/sciadv.abb3446},
number = {26},
journal = {Science Advances},
publisher = {American Association for the Advancement of Science (AAAS)},
author = {Ortiz, Cantin and Navarro, Jose Fernandez and Jurek, Aleksandra and Märtin, Antje and Lundeberg, Joakim and Meletis, Konstantinos},
year = {2020},
month = June
}Source: science.org ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB