CREMI Tools

Tools for the CREMI challenge and general neuron segmentation.

Setup

$ python setup.py install

TODO provide environment.yaml

Viewer

Provides convenience wrapper around volume viewe:

• volumina
• BigDataViewer
• Bigcat

Will install a script called view_container that can be used to display all volumes in a hdf5 or zarr/n5 container (file). Call via

$ view_container /path/to/container.h5

Alignment

TODO explain

Segmentation

TODO outdated? refactor?