spatial transcriptomics
Human heart
SPA42
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'SPA42_full_image': DataTree[cyx] (3, 8602, 9830), (3, 4301, 4915), (3, 2150, 2457), (3, 1075, 1228)
├── Shapes
│ └── 'SPA42_spots': GeoDataFrame shape: (159, 2) (2D shapes)
└── Tables
└── 'table': AnnData (159, 39739)
with coordinate systems:
▸ 'global', with elements:
SPA42_full_image (Images), SPA42_spots (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("8wgJjwSZg7bZ50us") # 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/8wgJjwSZg7bZ50us
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 8wgJjwSZg7bZ50us Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["8wgJjwSZg7bZ50us0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart→ 19 datasets · comparison
Metadata
- Technology
- spatial transcriptomics
- Organism
- human
- Tissue
- heart
- Modality
- RNA
- Observations
- 159
- Tier
- silver
- Chemistry
- ST 1k
- Resolution
- 9,830 × 8,602 px
- mpp
- 0.762 µm/px
- Size
- 123 MB
- Sample ID
- SPA42
- License
- CC BY-NC-SA 4.0 NonCommercial
- Published
- Dec 16, 2019
Cite this dataset
doi.org/10.1016/j.cell.2019.11.025 ↗ BibTeX
@article{Asp_2019,
title = {A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart},
volume = {179},
ISSN = {0092-8674},
url = {http://dx.doi.org/10.1016/j.cell.2019.11.025},
DOI = {10.1016/j.cell.2019.11.025},
number = {7},
journal = {Cell},
publisher = {Elsevier BV},
author = {Asp, Michaela and Giacomello, Stefania and Larsson, Ludvig and Wu, Chenglin and Fürth, Daniel and Qian, Xiaoyan and Wärdell, Eva and Custodio, Joaquin and Reimegård, Johan and Salmén, Fredrik and Österholm, Cecilia and Ståhl, Patrik L. and Sundström, Erik and Åkesson, Elisabet and Bergmann, Olaf and Bienko, Magda and Månsson-Broberg, Agneta and Nilsson, Mats and Sylvén, Christer and Lundeberg, Joakim},
year = {2019},
month = Dec,
pages = {1647–1660.e19}
}Source: sciencedirect.com ↗ · License: CC BY-NC-SA 4.0 ↗ · Reprocessed to SpatialData by SpatialData-DB