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

Deep pipe

A collection of utils for deep learning experiments.

Installation:

git clone https://github.com/neuro-ml/deep_pipe.git
cd deep_pipe
pip install -e .

Basic usage

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

Requirements

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

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