The project contains jupyter notebook about bio-image-analysis. Beakerx will be used to allow mixing python and java.
Note: The parts that launch the ImageJ gui interface from a notebook will only work when you run it locally, not on the server via mybinder.
You need to have anaconda and FIJI installed. Clone the repository.
From the directory containing the file env.yml call conda env create -f env.yml. Once the environment is installed, activate it with source activate beaker. Run jupyter notebook with the command beakerx.
Follow the instructions in the notebook to access ImageJ and python.