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README.md

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+# Loki
+Building on OmiCLIP, a visual–omics foundation model designed to bridge omics data and hematoxylin and eosin (H&E) images, we developed the **Loki** platform, which has five key functions: tissue alignment using ST or H&E images, cell type decomposition of ST or H&E images using scRNA-seq as a reference, tissue annotation of ST or H&E images based on bulk RNA-seq or marker genes, ST gene expression prediction from H&E images, and histology image–transcriptomics retrieval.
+
+This README provides a quick overview of how to set up and use Loki.
+
+The pre-train weights, source code, and ST-bank database will be released on GitHub and Hugging Face after the manuscript is accepted.
+
+
+## User Manual and Notebooks
+You can view the Loki website and notebooks locally by dobule clicking the `./website/index.html` file. It should show up in your default browser.
+
+
+
+## Source Code
+All source code for Loki is contained in the `./src/loki` directory.
+
+The source code will be released in GitHub and Hugging Face after the manuscript is accepted
+
+
+
+## Installation (It takes about 5 mins to finish the installation on MacBook Pro)
+
+1. **Create a Conda environment**:
+   ```bash
+   conda create -n loki_env python=3.9
+   conda activate loki_env
+   ```
+
+2. **Navigate to the Loki source directory and install Loki**:
+   ```bash
+   cd ./src
+   pip install .
+   ```
+
+
+## Usage
+Once Loki is installed, you can import it in your Python scripts or notebooks:
+   ```python
+   import loki.preprocess
+   import loki.utils
+   import loki.plot
+
+   import loki.align
+   import loki.annotate
+   import loki.decompose
+   import loki.retrieve
+   import loki.predex
+   ```
+
+
+
+## STbank
+The ST-bank database are avaliable from [Google Drive link](https://drive.google.com/drive/folders/1J15cO-pXTwkTjRAR-v-_nQkqXNfcCNn3?usp=sharing).
+
+The links_to_raw_data.xlsx file includes the source paper names, doi links, and download links of the raw data.
+The text.csv file includes the gene sentences with paired image patches.
+The image.tar.gz includes the image patches.
+
+The ST-bank database will be released in GitHub and Hugging Face after the manuscript is accepted.
+
+
+## Pretrained weights
+The pretrained weights are avaliable from [Google Drive link](https://drive.google.com/file/d/1UTJKAqoiUT55h9sA1Ee8iJeOclNLBvWD/view?usp=sharing).
+
+The pretrained weights will be released in GitHub and Hugging Face after the manuscript is accepted.
+
+
+
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 license: bsd-3-clause
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