| --- |
| 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 |
| ``` |
|
|
