pretrained and instructions for annotating and training segmentation of bacterial fluorescent images
Create environment:
conda create --name napari-env
conda activate napari-env
conda install -c conda-forge napari
conda install opencv
Install Tensorflow for macOS M1/M2:
pip install tensorflow-macos
pip install tensorflow-metal
Install stardist for cell segmentation:
pip install gputools
pip install stardist
pip install csbdeep
pip install splinedist
python augment_image_data.py
python training.py
Open up tensorboard to follow the results:
tensorboard --logdir=.
python prediction.py './input/' './output'