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license: bsd-3-clause |
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# Loki |
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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. |
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Please find our preprint [here](https://doi.org/10.21203/rs.3.rs-5183775/v1). |
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## User Manual and Notebooks |
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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. |
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This README provides a quick overview of how to set up and use Loki. |
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## Source Code |
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All source code for Loki is contained in the `./src/loki` directory. |
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## Installation (It takes about 5 mins to finish the installation on MacBook Pro) |
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1. **Create a Conda environment**: |
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```bash |
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conda create -n loki_env python=3.9 |
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conda activate loki_env |
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``` |
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2. **Navigate to the Loki source directory and install Loki**: |
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```bash |
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cd ./src |
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pip install . |
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``` |
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## Usage |
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Once Loki is installed, you can import it in your Python scripts or notebooks: |
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```python |
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import loki.preprocess |
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import loki.utils |
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import loki.plot |
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import loki.align |
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import loki.annotate |
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import loki.decompose |
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import loki.retrieve |
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import loki.predex |
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``` |
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## STbank |
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The ST-bank database are avaliable from [Google Drive link](https://drive.google.com/drive/folders/1J15cO-pXTwkTjRAR-v-_nQkqXNfcCNn3?usp=share_link). |
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The links_to_raw_data.xlsx file includes the source paper names, doi links, and download links of the raw data. |
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The text.csv file includes the gene sentences with paired image patches. |
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The image.tar.gz includes the image patches. |
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## Pretrained weights |
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The pretrained weights are avaliable in Loki/checkpoint.pt |
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--- |
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license: bsd-3-clause |
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--- |
