Python Library for ERL Evaluation

ERL Evaluation

• Installation

  
  # create a new environment
  conda create -n erl-eval python==3.9.0
  source activate erl-eval
  conda install -c conda-forge -c ostrokach-forge -c pkgw-forge graph-tool

clone the repo

git clone --recursive https://github.com/PytorchConnectomics/AxonEM-challenge.git

install funlib.evaluate

cd challenge_eval/funlib.evaluate pip install -r requirements.txt python setup.py install cd ..

(Under `challenge_eval/` folder)
- AxonEM evaluation: `python test_axonEM.py -s seg_axonM.h5 -g axonM_gt_16nm_skel_stats.p -c 5`

### Generate Skeleton
- install [kimimaro](https://github.com/seung-lab/kimimaro)

pip3 install kimimaro

(Under `challenge_eval/` folder)
- GT skeleton generation: `python skeleton.py -s snemi_train-labels.tif -r 30x6x6 -i 1,2,3 -o snemi_skel.p`
- ERL evaluation: `python test_volume.py -s pred_seg.tif -g snemi_skel.p -gu physical -gr 30x6x6`