.. loki documentation master file, created by
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Loki documentation
==================


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, tissue annotation of ST or H&E images based on bulk RNA-seq or marker genes, cell type decomposition of ST or H&E images using scRNA-seq as a reference, histology image–transcriptomics retrieval, and ST gene expression prediction from H&E images.

Please find our Nature Methods paper "A visual–omics foundation model to bridge histopathology with spatial transcriptomics" `here <https://www.nature.com/articles/s41592-025-02707-1>`_.

Please find our github `here <https://github.com/GuangyuWangLab2021/Loki>`_.


.. .. image:: images/loki_platform_image1.png
..   :width: 100%


.. image:: images/OmiCLIP_Loki.png
  :width: 100%


.. toctree::
   :maxdepth: 2
   :caption: ST-bank database

   ST-bank



.. toctree::
   :maxdepth: 2
   :caption: Pretrained weights

   pretrain



.. toctree::
   :maxdepth: 2
   :caption: Loki

   API



.. .. image:: images/loki_platform_image2.png
..    :width: 60%



.. toctree::
   :maxdepth: 2
   :caption: Tutorials

   notebooks/Installation
   notebooks/basic_usage
   notebooks/Loki_Align_case_study_8_small_intestine
   notebooks/Loki_Align_case_study_2_OCS
   notebooks/Loki_Annotate_case_study_bulk_RNAseq
   notebooks/Loki_Annotate_case_study_marker_genes
   notebooks/Loki_Decompose_case_study_TNBC
   notebooks/Loki_Decompose_case_study_CRC
   notebooks/Loki_Retrieve
   notebooks/Loki_PredEx_case_study