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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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The pre-train weights, source code, and ST-bank database will be released on GitHub and Hugging Face after the manuscript is accepted.
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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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## Source Code
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All source code for Loki is contained in the `./src/loki` directory.
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The source code will be released in GitHub and Hugging Face after the manuscript is accepted
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## Installation (It takes about 5 mins to finish the installation on MacBook Pro)
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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=
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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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---
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license: bsd-3-clause
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---
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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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## 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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