Segmantic

Segmantic is a MONAI/PyTorch-based library for medical image segmentation.

Features

• utilities to prepare datasets for use in training of segmentation and style transfer networks
• segmentation networks
• evaluation metrics (fast confusion matrix, Hausdorff distance, ...)
• image to image translation (based on pix2pix / cyclegan) to help generalization from limited training data

Installation

Create a virtual environment

cd /your/working/directory
python -m venv .venv

Activate it using e.g. source .venv/bin/activate on Linux/Mac and .venv\Scripts\activate.bat on Windows.

To install this repo (this will install all dependencies):

pip install git+https://github.com/dyollb/segmantic.git#egg=segmantic

Or in edit/dev mode

pip install -e git+https://github.com/dyollb/segmantic.git#egg=segmantic[dev]

Getting started

The project layout is as follows:

|-- segmantic/src/segmantic
    |-- commands   # command lines
    |-- i2i        # image-to-image translation (style transfer)
    |-- prepro     # module containing utils to prepare your data
    |-- seg        # semantic segmentation: training, inference and evaluation
    |-- util       # utility functions
|-- segmantic/pyproject.toml
|-- segmantic/scripts
|-- segmantic/tests