Co-registration of multiplexed images

File structure

• stitch_nd2 Python script for performing tile stitching of Nikon ND2 data and converting the result to OME-TIFF format.
• coregistration_qupath Tutorial describing how to perform co-registration of a mix of single-channel and multi-channel OME-TIFF files using Warpy in QuPath.

Python installation (via Anaconda and pip):

1. Install the Anaconda (Miniconda) package manager for Python 3.9 from here. On Linux, you can also install it like this:

    curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh  
    sh Miniconda3-latest-Linux-x86_64.sh

2. Create a new virtual environment (coregistration) for the application, from the terminal or Anaconda command line:

    conda create --name coregistration python=3.9

3. Activate the virtual environment and install the required Python dependendecies (via pip):

    conda activate coregistration
    pip install -r requirements.txt

Usage

See the respective README.md file or documentation in each subfolder.

License

The code is provided under the MIT license (see LICENSE.md).