This repository contains the implementation of the paper available on OpenReview.

To get started, follow these steps:

1. Clone the repository:

   git clone https://github.com/jichunxie/xMINT_manu_support
   cd xMINT_manu_support

2. Create a Conda environment with Python 3.8:

   conda create -n xmint_env python=3.8
   conda activate xmint_env

3. Install the required packages using the requirements.txt file:

   pip install -r requirements.txt

You will need paired Xenium datasets from the same tissue to get started.

For each dataset, the input data should include:

1. Xenium Output Bundle: The data generated by Xenium.
2. Post-Xenium H&E Image: An OME-TIFF file of the H&E stained image corresponding to the Xenium output.

Unzip the Xenium Output Bundle folder and place the H&E image into the output folder.

Our paper utilized the following datasets:

• FFPE Human Breast with Pre-designed Panel 1 Standard
• Human Tonsil Data: Xenium Human Multi-Tissue and Cancer Panel 1 Standard

To run the pipeline, follow these steps:

1. Run the preprocessing script:

   python preprocess_to_sequence.py

2. Run the main xMINT script:

   python xmint_main.py

Before running these scripts, ensure you update the sample names and other customized parameters as needed.