xbrain-py

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.

Getting started...

(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!

• Run entire cell detection + vessel segmentation workflow on small cube of brain data (notebook)
• Run simple ilastik classifier on large volumes (notebook)

Contributors

• Eva Dyer (@evadyer)
• Will Gray Roncal (@willgray)
• Mehdi Tondravi (@anlmehdi)