Collections / A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart

A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart

Datasets19
Size~3.1 GB
Assayspatial transcriptomics
Samplehuman · heart
KindComparison
Flag a data issue
10.1016/j.cell.2019.11.025 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("doi-10-1016-j-cell-2019-11-025")
cohort.members        # the 19 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")
Install (Python 3.12+) Docs →
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")
coll = db.Collection.get(key="doi-10.1016/j.cell.2019.11.025")
coll.ordered_artifacts.to_dataframe()   # the 19 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection doi-10-1016-j-cell-2019-11-025 --dest data/
Install (Python 3.12+) Docs →

Licenses: 19 CC BY-NC-SA 4.0

About the study

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

Read the abstract at the source →
Member datasets · 19
Open in Vitessce
spatial transcriptomics
Human heart
SPA34
human heart 203 MB 242 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size203 MB
Spots242
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA31
human heart 208 MB 198 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size208 MB
Spots198
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA32
human heart 200 MB 226 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size200 MB
Spots226
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA42
human heart 129 MB 159 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size129 MB
Spots159
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA46
human heart 223 MB 69 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size223 MB
Spots69
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA43
human heart 111 MB 104 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size111 MB
Spots104
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA33
human heart 105 MB 243 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size105 MB
Spots243
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA45
human heart 132 MB 55 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size132 MB
Spots55
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA47
human heart 147 MB 59 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size147 MB
Spots59
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA36
human heart 206 MB 180 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size206 MB
Spots180
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA48
human heart 162 MB 55 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size162 MB
Spots55
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA40
human heart 191 MB 214 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size191 MB
Spots214
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA38
human heart 204 MB 178 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size204 MB
Spots178
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA39
human heart 113 MB 209 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size113 MB
Spots209
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA44
human heart 147 MB 103 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size147 MB
Spots103
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA35
human heart 136 MB 238 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size136 MB
Spots238
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA41
human heart 178 MB 186 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size178 MB
Spots186
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA37
human heart 117 MB 182 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size117 MB
Spots182
silver H&E Open in Vitessce
Open in Vitessce
spatial transcriptomics
Human heart
SPA30
human heart 215 MB 211 spots silver H&E
Technologyspatial transcriptomics
Organismhuman
Tissueheart
Size215 MB
Spots211
silver H&E Open in Vitessce

Cite this collection

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}
}