epyseg 0.1.1

A deep learning based tool to segment epithelial tissues. The epyseg GUI can be uesd to build, train or run custom networks

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