spatial transcriptomics
Human heart
SPA35
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'SPA35_full_image': DataTree[cyx] (3, 8602, 9830), (3, 4301, 4915), (3, 2150, 2457), (3, 1075, 1228)
├── Shapes
│ └── 'SPA35_spots': GeoDataFrame shape: (238, 2) (2D shapes)
└── Tables
└── 'table': AnnData (238, 39739)
with coordinate systems:
▸ 'global', with elements:
SPA35_full_image (Images), SPA35_spots (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("5YaKaF4fzPr9rrdp0000")
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("5YaKaF4fzPr9rrdp") # 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 5YaKaF4fzPr9rrdp0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5YaKaF4fzPr9rrdp
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5YaKaF4fzPr9rrdpLicense: CC BY-NC-SA 4.0 (noncommercial)
Part 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 (spots)
- 238
- Tier
- silver
- Chemistry
- ST 1k
- Resolution
- 9,830 × 8,602 px
- mpp
- 0.908 µm/px
- Size
- 136 MB
- Sample ID
- SPA35
- 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