This repository is deprecated, have a look at cluster_tools instead.
Multicut workflow for large connectomics data. Using luigi for pipelining and caching processing steps. Most of the computations are done out-of-core using hdf5 as backend and implementations from nifty
You need a cplex or gurobi license to use the multicut pipeline.
To fulfill all dependencies, you also need to have the ilastik and conda-forge channel in your .condarc . Then install the package via
$ GUROBI_ROOT_DIR=/path/to/gurobi conda install -c cpape mc_luigi=0.1
The current package only supports gurobi as solver backend, please make an issue if you need a version with cplex.
You can also install the dependencies from source:
- Luigi: https://github.com/spotify/luigi (version 2.3)
- Vigra: https://github.com/ukoethe/vigra (master, needs to be build with hdf5 and python-bindings)
- Nifty: https://github.com/constantinpape/nifty/tree/stacked_rag , needs to be build with python-bindings, hdf5, fastfilters (https://github.com/svenpeter42/fastfilters) and Gurobi or CPLEX.
- Lifted Multicut
- Pipeline for isotropic data.
- Get central scheduler running.
- Add docstrings
- change to PEP8 style