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README.md
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- spatial-domains
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---
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Full [`novae`](https://github.com/MICS-Lab/novae) dataset, including:
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1. All the spatial transcriptomics samples used to train Novae
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2. Protein samples used in the article
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See [here](https://huggingface.co/collections/MICS-Lab/novae-669cdf1754729d168a69f6bd) the list of available models trained on this dataset.
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> [!NOTE]
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> 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.
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- spatial-domains
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---
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## Description
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Full [`novae`](https://github.com/MICS-Lab/novae) dataset, including:
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1. All the spatial transcriptomics samples used to train Novae
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2. Protein samples used in the article
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See [here](https://huggingface.co/collections/MICS-Lab/novae-669cdf1754729d168a69f6bd) the list of available models trained on this dataset.
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> [!NOTE]
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> 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.
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## Cite us
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Our article is published in [Nature Methods](https://www.nature.com/articles/s41592-025-02899-6). You can cite Novae as below:
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```txt
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Blampey, Q., Benkirane, H., Bercovici, N. et al. Novae: a graph-based foundation model for spatial transcriptomics data.
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Nat Methods (2025). https://doi.org/10.1038/s41592-025-02899-6
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```
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