diff --git a/README.md b/README.md index ae63657..1d439cd 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,6 @@
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> **(a)** Novae was trained on a large dataset, and is shared on [Hugging Face Hub](https://huggingface.co/collections/MICS-Lab/novae-669cdf1754729d168a69f6bd). **(b)** Illustration of the main tasks and properties of Novae. **(c)** Illustration of the method behing Novae (self-supervision on graphs, adapted from [SwAV](https://arxiv.org/abs/2006.09882)). diff --git a/docs/index.md b/docs/index.md index b1b6b30..ef0eb72 100644 --- a/docs/index.md +++ b/docs/index.md @@ -2,4 +2,25 @@ -TODO ++ 💫 Graph-based foundation model for spatial transcriptomics data +
+ +Novae is a deep learning model for spatial domain assignments of spatial transcriptomics data (at both single-cell or spot resolution). It works across multiple gene panels, tissues, and technologies. Novae offers several additional features, including: (i) native batch-effect correction, (ii) analysis of spatially variable genes and pathways, and (iii) architecture analysis of tissue slides. + +## Overview + ++ +
+ +> **(a)** Novae was trained on a large dataset, and is shared on [Hugging Face Hub](https://huggingface.co/collections/MICS-Lab/novae-669cdf1754729d168a69f6bd). **(b)** Illustration of the main tasks and properties of Novae. **(c)** Illustration of the method behing Novae (self-supervision on graphs, adapted from [SwAV](https://arxiv.org/abs/2006.09882)). + + +## Why using Novae + +- It is already pretrained on a large dataset (pan human/mouse tissues, brain, ...). Therefore, you can compute spatial domains in a zero-shot manner (i.e., without fine-tuning). +- It has been developed to find consistent domain across many slides. This also work if you have different technologies (e.g., MERSCOPE/Xenium) and multiple gene panels. +- You can natively correct batch effect, without using external tools. +- After inference, the spatial domain assignment is super fast, allowing to try multiple resolutions easily. +- It supports many downstream tasks, all included inside one framework. diff --git a/pyproject.toml b/pyproject.toml index 60f1adf..ab170bb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "novae" -version = "0.0.2" +version = "0.0.5" description = "Graph-based foundation model for spatial transcriptomics data" documentation = "https://mics-lab.github.io/novae/" homepage = "https://mics-lab.github.io/novae/"