/deep_pipe

Repository for tools, useful for medical image analysis, including preprocessing, data augmentation, performance validation and final prediction

Primary LanguagePython

Deep pipe

Repository for deep learning experiments with 3d image segmentation

Installation:

git clone https://github.com/neuro-ml/deep_pipe.git

Then you need to add the library to the list of python libraries. One of the ways:

ln -s /path/to/deep_pipe/dpipe /path/to/virtualenv/lib/python3.6/site-packages/ # for virtualenv
# or
ln -s /path/to/deep_pipe/dpipe /path/to/anaconda/lib/python3.6/site-packages/ # for conda

Basic usage

  1. Create a config file. There are some examples in config_examples
  2. To build the experiment, run
python /path/to/deep_pipe/scripts/do.py build_experiment --config_path CONFIG_PATH --experiment_path EXPERIMENT_PATH
  1. To start the experiment, run
/path/to/deep_pipe/experiment/run_experiment_seq.sh EXPERIMENT_PATH

Requirements

Only Python 3.6 is supported for now. Other requirements are listed in requirements.txt.