Opal Unmixing

Script for working with QPTIFF files and Opal unmixing Sample AF from the other channels.

This will generate big image files! About 2-8Gb for non pyramidal images and 10-40Gb for pyramidal images.

Installation

Prerequisites

Required software: Python3, Java, Maven Recommended to use conda to manage environments.

Installation

This was only tested on Mac OS and Linux through docker. It should work on Windows, but it has not been tested.

Mac OS

    brew install miniconda openjdk maven temurin
    conda create --name opal python=3.12
    conda activate opal

Linux

   sudo apt-get install miniconda openjdk maven
   conda create --name opal python=3.12
   conda activate opal

Windows

Install miniconda, openjdk, and maven. Then create a new environment with python 3.12.

    conda create --name opal python=3.12
    conda activate opal

Clone the Repository

    git clone https://github.com/alex1075/Opal-unmixing.git
    cd Opal_unmixing

Install Python Dependencies

    pip install -r requirements.txt

Install Java dependencies using Maven

    mvn clean install

Running the Script

To run the script for unmixing channels in a QPTIFF file ONLY, use the following command:

    python unmix_convert.py <input_file> <output_file> <unmixing_matrix:optional>

To run the script for unmixing channels in a QPTIFF file and generate a pyramidal image, use the following command:

    python unmix_convert.py <input_file> <output_file> <unmixing_matrix:optional>

To Do

• Calculate unmixing matrix for all Opal dyes to unmix all channels (through single stain controls)
• Add unmixing to conver_with_pyramids
• Add support for other export file formats