/EPySeg

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

EPySeg

EPySeg is a package for segmenting 2D epithelial tissues. EPySeg also ships with a graphical user interface that allows for building, training and running deep learning models. Training can be done with or without data augmentation (2D-xy and 3D-xyz data augmentation is supported). EPySeg relies on the segmentation_models library. EPySeg sources are available here.

Install

  1. Install python 3.7 or Anaconda 3.7 (if not already present on your system)

  2. In a command prompt type:

    pip install --user --upgrade epyseg

    or

    pip3 install --user --upgrade epyseg

    NB:

    • To open a command prompt on Windows press 'Windows'+R then type 'cmd'
    • To open a command prompt on MacOS press 'Command'+Space then type in 'Terminal'

  3. To open the graphical user interface, type the following in a command:

    python -m epyseg

    or

    python3 -m epyseg