nilsec/n5_to_knossos

Convert n5 to knossos by converting to png stacks first (supported by cuber) and applying knossos cuber. Ugly but works.

0. Install requirements:

pip3 install -r requirements.txt

1. Install knossos cuber:

pip3 install https://github.com/knossos-project/knossos_cuber/archive/master.zip

2. Modify knossos cuber config by setting 'scaling' and 'boundary' to the n5 resolution and shape respectively. Can be done automatically if n5 meta data is consistent.

3. Run script

python n5_to_knossos.py --n5 path_to_n5 --dset dataset_name --png png_stack_output_dir --knossos knossos_output_dir --config cuber_config_file_path