---
license: bsd-3-clause
tags:
- spatial-data
- spatial-transcriptomics
- biology
- omics
- spatial-domains
---

## Description

Full [`novae`](https://github.com/MICS-Lab/novae) dataset, including:
1. All the spatial transcriptomics samples used to train Novae
2. Protein samples used in the article
3. Some Visium and Visium HD samples
4. Synthetic data samples

You can download this dataset from the API, see [`novae.load_dataset`](https://mics-lab.github.io/novae/api/data/#novae.load_dataset)

See [here](https://huggingface.co/collections/MICS-Lab/novae-669cdf1754729d168a69f6bd) the list of available models trained on this dataset.

> [!NOTE]
> 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](https://www.nature.com/articles/s41592-025-02899-6). You can cite Novae as below:

```txt
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
```