python tools for segmenting X-ray brain volumes
This is the python implementation of the methods described and visualized here. If you use any of these tools, please cite our paper. If you have any questions, please contact Eva Dyer at Eva.L.Dyer {at} gmail {dot} com.
(Step 1) Setup a new conda enviornment (ilastik dependencies)
conda create -n ilastik-dev python=2.7
source activate ilastik-dev
conda install -c ilastik ilastik-everything-but-tracking
pip install ndparse
pip install mahotas
conda remove tifffile
conda install -c ilastik tifffile=0.4.1
conda install ipython
conda install jupyter
pip install tifffiles
source deactivate
Now each time you run ilastik, you need to enter into this environment. To start the environment and launch a notebook, use the following (terminal) command:
source activate ilastik-dev
jupyter notebook
(Step 2) Run one of our example notebooks!