Deep Cell

Reimplement Deep Cell with Keras and Horovod. The paper of Deep Cell is here.

Dataset

Download the Dataset:

./get_dataset.sh

Enviroment

If you use pip to manage your Python enviroment:

pip install -r requirements.txt

If you use conda as your Python enviroment:

conda env create -f environment.yml

Usage

The sub-command can be

1. data_prepare
2. train
3. validation
4. test

Or you can use pipeline as sub-command to run all 4 steps.

python launch.py pipeline

Tips

• We use "channels_first" date format in Keras, you should config in ~/.keras/keras.json.

• If you want to run a distributed training, you must install Horovod and run

   mpirun -np 4 python deepcell/train.py -e 20 --dist 1

Thanks

DeepCell and deepcell-tf