Integrated analysis platform of tissue histology and spatial transcriptomics at the cell level

Thor enables cell-level spatial transcriptomics analysis by integrating histology and transcriptomic information through an anti-shrinking Markov diffusion method.

Key features:

• Jointly leverages histological and transcriptomic information for accurate inference
• Achieves single-cell resolution without requiring additional single-cell reference data

.. image:: _static/workflow_part1.png :width: 100% :alt: workflow

Thor modules

.. image:: _static/Thor_advanced_analysis_illustration.png :width: 100% :alt: function

What's new

• 🚀 2025-09-16: Added tutorial for running copy number aberration in the notebooks/ <./notebooks>_ directory
• 🚀 2025-09-03: Updated preprocessing scripts for Visium HD data and added a new tutorial in the visiumhd/ <./visiumhd>_ directory
• 🧬 Added full support for Visium HD data
• 🔗 Integrated COMMOT for cell–cell communication analysis

Installation

Thor is written in Python (3.9+) and tested on macOS and Linux. We recommend installing it inside a virtual environment.

Step 1. Create a virtual environment (recommended)

Using conda <https://docs.conda.io/en/latest/>__:

.. code-block:: bash

conda create -n Thor python=3.9 conda activate Thor

Step 2. Clone the repository

.. code-block:: bash

git clone https://github.com/GuangyuWangLab2021/Thor.git cd Thor

Step 3. Install Thor

• Base installation:

  .. code-block:: bash

  pip install .

• With optional visualization and advanced analysis:

  .. code-block:: bash

  pip install ".[vis,analysis]"

Cell–cell communication (COMMOT)

Currently, Thor includes COMMOT, a state-of-the-art tool for spatial communication analysis. This module is under active development, and we welcome feedback and contributions.

Requirements:

• R (tested with version 4.2.2)

• Python dependencies:

  .. code-block:: bash

  pip install --no-deps commot@git+https://github.com/biopzhang/COMMOT.git pip install karateclub@git+https://github.com/benedekrozemberczki/karateclub.git POT libpysal rpy2==3.5.11 anndata2ri==1.2

Usage

• Visit the Thor website <https://wanglab.tech/thor>__ for API documentation and tutorials
• Launch the Mjolnir web app for interactive visualization of WSIs and Thor outputs: https://wanglab.tech/mjolnir_launch/ <https://wanglab.tech/mjolnir_launch/>__
• To reproduce the results in our paper, see the tutorials and parameters in the parameters <./parameters/>_ directory

Frequently Asked Questions

(Coming soon – please open an issue if you have questions you’d like us to cover!)

Support

Please report bugs, request features, or share feedback on the GitHub Issues page <https://github.com/GuangyuWangLab2021/Thor/issues>__.