Workflows for distributed Bio Image Analysis and Segmentation. Supports Slurm, LSF and local execution, easy to extend to more scheduling systems.

• Hierarchical (lifted) Multicut
  • Distance Transform Watersheds
  • Region Adjacency Graph
  • Edge Feature Extraction from Boundary-or-Affinity Maps
  • Agglomeration via (lifted) Multicut
• Mutex Watershed
• Connected Components
• Downscaling and Pyramids
  • Paintera Format
  • BigDataViewer Format
  • Bigcat Format
• Ilastik Prediction
• Skeletonization
• Distributed Neural Network Prediction (originally implemented here)

All dependencies can be installed via conda, using the environment.yml file:

conda env create -f environment.yml

For now, this only supports linux and python3.7. The package itself must be added to the python environment manually, e.g. by creating a softlink in the lib/python3.7/site-packages of the conda env.