metadata
license: bsd-3-clause
tags:
- spatial-data
- spatial-transcriptomics
- biology
- omics
- spatial-domains
Description
Full novae dataset, including:
- All the spatial transcriptomics samples used to train Novae
- Protein samples used in the article
- Some Visium and Visium HD samples
- Synthetic data samples
You can download this dataset from the API, see novae.load_dataset
See here the list of available models trained on this dataset.
Note that Novae was trained on the image-based spatial transcriptomics samples. This means that it was not trained on the Visium/VisiumHD samples and the spatial proteomics samples.
Cite us
Our article is published in Nature Methods. You can cite Novae as below:
Blampey, Q., Benkirane, H., Bercovici, N. et al. Novae: a graph-based foundation model for spatial transcriptomics data.
Nat Methods (2025). https://doi.org/10.1038/s41592-025-02899-6