The Myoblast Fusion Index Determination Software

The MyoFInDer Python package aims to provide an open-source graphical interface for automatic calculation of the fusion index in muscle cell cultures, based on fluorescence microscopy images.

[!IMPORTANT] MyoFInDer is currently in maintenance-only development phase. This means that reported bugs will be fixed, minor changes will be brought to support new Python versions if possible, but no major improvements or updates should be expected. User requests for new features could still be addressed, depending on how large they are.

[!WARNING] MyoFInDer version 1.1.0 now uses CellPose for nuclei segmentation instead of DeepCell. This is a major breaking change. Differences are to be expected in the results obtained with version 1.1.0 and earlier ones, even with similar processing parameters.

Presentation

MyoFInDer is based on an Artificial Intelligence library for cell segmentation, that it makes easily accessible to researchers with limited computer skills. In the interface, users can manage multiple images at once, adjust processing parameters, and manually correct the output of the computation. It is also possible to save the result of the processing as a project, that can be shared and re-opened later.

A more detailed description of the features and usage of MyoFInDer can be found in the usage section of the documentation.

MyoFInDer was developed at the Tissue Engineering Lab in Kortrijk, Belgium, which is part of the KU Leuven university. It is today the preferred solution in our laboratory for assessing the fusion index of a cell population.

Requirements

To install and run MyoFInDer, you'll need Python 3 (3.10 to 3.14), approximately 6GB of disk space, and preferably 8GB of memory or more. MyoFInDer runs on Windows, Linux, macOS, and potentially other OS able to run a compatible version of Python.

The dependencies of the module are :

• Pillow
• opencv-python
• CellPose
• XlsxWriter
• screeninfo
• numpy

For each supported platform, architecture, and Python version, a requirements file can be found in the requirements folder of this repository. MyoFInDer is tested using these specific sets of dependencies.

Installation

MyoFInDer is distributed on PyPI, and can thus be installed using the pip module of Python :

python -m pip install myofinder

Note that in the bin folder of this repository, a very basic .msi Windows installer allows automatically installing the module and its dependencies for Windows users who don't feel comfortable with command-line operations.

Also, the simple pip install command is likely to fail on Python versions more recent than 3.12. In this case, installing the recommended requirements file first and then myofinder with the --no-deps option is recommended.

A more detailed description of the installation procedure can be found in the installation section of the documentation.

Citing MyoFInDer

If MyoFInDer has been of help in your research, please reference it in your academic publications by citing the following article:

• Weisrock A., Wüst R., Olenic M. et al., MyoFInDer: An AI-Based Tool for Myotube Fusion Index Determination, Tissue Eng. Part A (30), 19-20, 2024, DOI: 10.1089/ten.TEA.2024.0049. (link to Weisrock et al.)

Documentation

The latest version of the documentation can be accessed on the project's website. It contains detailed information about the installation, usage, and troubleshooting.