myofinder 1.0.9

Automatic calculation of the fusion index by AI segmentation

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.

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 (3.7 to 3.10), approximately 1GB 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
• DeepCell
• XlsxWriter
• screeninfo
• numpy

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.

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

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.