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

Project description

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 are supported). EPySeg relies on the segmentation_models library. EPySeg source code is available here. Cloud version 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
    

Third party libraries

Below is a list of the 3rd party libraries used by EPySeg and/or pyTA.

<font color='red'>IMPORTANTLY: if you disagree with any license below, <u>please uninstall EPySeg</u>.
</font>

Library name Use Link License
tensorflow Deep learning library https://pypi.org/project/tensorflow/ Apache 2.0
segmentation-models Models https://pypi.org/project/segmentation-models/ MIT
czifile Reads Zeiss .czi files https://pypi.org/project/czifile/ BSD (BSD-3-Clause)
Markdown Python implementation of Markdown https://pypi.org/project/Markdown/ BSD
matplotlib Plots images and graphs https://pypi.org/project/matplotlib/ PSF
numpy Array/Image computing https://pypi.org/project/numpy/ BSD
numpydoc Numpy documentation format https://pypi.org/project/numpydoc/ BSD
Pillow Reads 'basic' images (.bmp, .png, .pnm, ...) https://pypi.org/project/Pillow/ HPND
PyQt5 Graphical user interface (GUI) https://pypi.org/project/PyQt5/ GPL v3
PyQtWebEngine Display html in GUI https://pypi.org/project/PyQtWebEngine/ GPL v3
read-lif Reads Leica .lif files https://pypi.org/project/read-lif/ GPL v3
scikit-image Image processing https://pypi.org/project/scikit-image/ BSD (Modified BSD)
scipy Great library to work with numpy arrays https://pypi.org/project/scipy/ BSD
tifffile Reads .tiff files (also reads Zeiss .lsm files) https://pypi.org/project/tifffile/ BSD
tqdm Command line progress https://pypi.org/project/tqdm/ MIT, MPL 2.0
natsort 'Human' like sorting of strings https://pypi.org/project/natsort/ MIT
numexpr Speeds up image math https://pypi.org/project/numexpr/ MIT
urllib3 Model architecture and trained models download https://pypi.org/project/urllib3/ MIT
qtawesome Elegant icons in pyTA https://pypi.org/project/QtAwesome/ MIT
pandas Data analysis toolkit https://pypi.org/project/pandas/ BSD (BSD-3-Clause)
numba GPU acceleration of numpy ops https://pypi.org/project/numba/ BSD
elasticdeform Image deformation (data augmentation) https://pypi.org/project/elasticdeform/ BSD
CARE/csbdeep pyTA uses custom trained derivatives of the CARE surface projection model to generate (denoised) surface projections https://pypi.org/project/csbdeep/ BSD (BSD-3-Clause)

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